Discussion:
[Gmod-gbrowse] [Gmod-help] Can I ask a question of Gbrowse2?
Scott Cain
2012-04-24 13:45:13 UTC
Permalink
Hello Jiantao,

What you are seeing is almost always a result of the config and the
data not matching. I think your "group_on" setting is incorrect; it
is usually something like "group_on = display_name" or "group_on =
subject". I don't think setting it equal to the name of the feature
type does anything. If fixing that doesn't work, you could send a
sample of the GFF to the list. Also, there is a section of the
tutorial that came with GBrowse that covers xyplots that might help
(look for "quantitative data" in the tutorial).

Scott
Dear Sir/Madam,
I highly appreciate the smart of GBrowse. When I tried to display the
quantitative data, and set up the zoom with small values, such as 40Kbp, I
got the picture as is attached (picture1.png). However, I perfer the blocks
to locate on the same line, rather than being hierarchical. I mean, It would
be better if the blocks are kept as they are in the zoom of 500Kbp (all of
the blocks are at one line, shown in the picture2.png). Could you please
tell me how to do this? Many thanks!
[methySW_MSH1_1000K]
feature         = methySW_MSH1_1000K
glyph           = xyplot
graph_type      = boxes
fgcolor         = red
bgcolor         = red
height          = 80
min_score       = 0
max_score       = 1
scale           = none
group_on        = methySW_MSH1_1000K
category        = Quantitative Data
label           = 0
key             = Methylation Profile - MSH1_dr_vs_Col0 (Sliding
Windows:1000K-size)
Best wishes,
Jiantao
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
Scott Cain
2012-04-24 16:02:47 UTC
Permalink
Hi Jiantao,

"subject" should work for your data. Did you try panning or zooming
to another location to make sure GBrowse wasn't using a cached image
(just reloading isn't enough)?

Scott
Hi Scott,
Really thanks for you quick reply. I tried to change group-on in the config
file into
group_on = display_name                    or
group_on =subject
However, it seems no effect. I have attached the .gff3 and .conf files, and
the configure script for the .gff3 data starts at the line of No.1365.
Could you please have a look at them? Thanks very much.
Best regards
Jiantao
Post by Scott Cain
Hello Jiantao,
What you are seeing is almost always a result of the config and the
data not matching.  I think your "group_on" setting is incorrect; it
is usually something like "group_on = display_name" or "group_on =
subject".  I don't think setting it equal to the name of the feature
type does anything.  If fixing that doesn't work, you could send a
sample of the GFF to the list.  Also, there is a section of the
tutorial that came with GBrowse that covers xyplots that might help
(look for "quantitative data" in the tutorial).
Scott
Dear Sir/Madam,
I highly appreciate the smart of GBrowse. When I tried to display the
quantitative data, and set up the zoom with small values, such as 40Kbp, I
got the picture as is attached (picture1.png). However, I perfer the blocks
to locate on the same line, rather than being hierarchical. I mean, It would
be better if the blocks are kept as they are in the zoom of 500Kbp (all of
the blocks are at one line, shown in the picture2.png). Could you please
tell me how to do this? Many thanks!
[methySW_MSH1_1000K]
feature         = methySW_MSH1_1000K
glyph           = xyplot
graph_type      = boxes
fgcolor         = red
bgcolor         = red
height          = 80
min_score       = 0
max_score       = 1
scale           = none
group_on        = methySW_MSH1_1000K
category        = Quantitative Data
label           = 0
key             = Methylation Profile - MSH1_dr_vs_Col0 (Sliding
Windows:1000K-size)
Best wishes,
Jiantao
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
Scott Cain
2012-04-27 15:33:53 UTC
Permalink
Jiantao,

Please always respond to the mailing list too (reply-all).

No, you absolutely should not try to group these features by ID. That
will result in the database loader putting all of the features
together into one gigantic object in the database, and your
performance will be very poor (GBrowse may stop rendering those tracks
altogether). I'll try to reproduce your problem now.

Scott
Hi Scott,
I still got the picture like the attahed file, although I changed
group_on=subject. Do you think I need to add 'ID=1' for all of the entries
in .gff3 file, in order to let them displayed on the single line?
GBrowse may group entries according to their IDs? However, when I did this,
I can't get the specific balloon for each position/block in the picture, you
see, I just got a very general description in the balloon, such as this
position is from 1..30Mbp, which is not what I want to get.
Thanks a lot.
Jiantao
Post by Scott Cain
Hi Jiantao,
"subject" should work for your data.  Did you try panning or zooming
to another location to make sure GBrowse wasn't using a cached image
(just reloading isn't enough)?
Scott
Hi Scott,
Really thanks for you quick reply. I tried to change group-on in the config
file into
group_on = display_name                    or
group_on =subject
However, it seems no effect. I have attached the .gff3 and .conf files, and
the configure script for the .gff3 data starts at the line of No.1365.
Could you please have a look at them? Thanks very much.
Best regards
Jiantao
Post by Scott Cain
Hello Jiantao,
What you are seeing is almost always a result of the config and the
data not matching.  I think your "group_on" setting is incorrect; it
is usually something like "group_on = display_name" or "group_on =
subject".  I don't think setting it equal to the name of the feature
type does anything.  If fixing that doesn't work, you could send a
sample of the GFF to the list.  Also, there is a section of the
tutorial that came with GBrowse that covers xyplots that might help
(look for "quantitative data" in the tutorial).
Scott
On Mon, Apr 23, 2012 at 8:14 PM, Jiantao Yu
Dear Sir/Madam,
I highly appreciate the smart of GBrowse. When I tried to display the
quantitative data, and set up the zoom with small values, such as 40Kbp,
I
got the picture as is attached (picture1.png). However, I perfer the blocks
to locate on the same line, rather than being hierarchical. I mean, It
would
be better if the blocks are kept as they are in the zoom of 500Kbp (all
of
the blocks are at one line, shown in the picture2.png). Could you please
tell me how to do this? Many thanks!
[methySW_MSH1_1000K]
feature         = methySW_MSH1_1000K
glyph           = xyplot
graph_type      = boxes
fgcolor         = red
bgcolor         = red
height          = 80
min_score       = 0
max_score       = 1
scale           = none
group_on        = methySW_MSH1_1000K
category        = Quantitative Data
label           = 0
key             = Methylation Profile - MSH1_dr_vs_Col0 (Sliding
Windows:1000K-size)
Best wishes,
Jiantao
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
Scott Cain
2012-04-27 16:42:20 UTC
Permalink
Hi Jiantao,

I forgot to ask--what version of GBrowse are you using? Your conf
file looks like GBrowse 1.X. Also, I trimmed the GMOD help desk email
off the cc list.

For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine. There is a
problem either with your data, your config or both. I'm working on a
simplified case to see if I can reproduce your problem.

For the key/track title problem, I'm guessing you had illigal characters.

Scott
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think, would be
the boxes are too close. For example, if the start and end positions are
1    10    0.8    .    .
11    20    0.7    .    .
21    30    0.7    .    .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4    7    0.8    .    .
14    17    0.7    .    .
24    27    0.7    .    .
They would be on the same line. However, in the case of my data, it is hard
to determine what values should be added or subtracted. For example, I used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure all of
the boxes are on the same line for every scale of zooming in or zooming out.
Jiantao Yu
2012-04-27 16:51:23 UTC
Permalink
Hi Scott,

I think I am using Gbrowse2, and I made the configure file based on your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.

However, I am not 100 percent sure of this. Can you tell me how can I check
the version of Gbrowse.

Another point is that, you see, GBrowse2 didn't provide the configure file
of Arabidopsis, so we generated this file by ourselves. However, the file
is made by my colleague, so I am not sure if he took this configure file
from the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is
from GBrowse1.x, I will ask my colleague and make sure of this. Thanks.

Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using? Your conf
file looks like GBrowse 1.X. Also, I trimmed the GMOD help desk email
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine. There is a
problem either with your data, your config or both. I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal characters.
Scott
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think, would
be
the boxes are too close. For example, if the start and end positions are
1 10 0.8 . .
11 20 0.7 . .
21 30 0.7 . .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4 7 0.8 . .
14 17 0.7 . .
24 27 0.7 . .
They would be on the same line. However, in the case of my data, it is
hard
to determine what values should be added or subtracted. For example, I
used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure
all of
the boxes are on the same line for every scale of zooming in or zooming
out.
Scott Cain
2012-04-27 17:04:54 UTC
Permalink
Hi Jiantao,

The easiest way to tell what version of GBrowse you are using is the
location of the config files: if they are int /etc/gbrowse, it's
GBrowse2. If not, it's probably GBrowse 1.

Since part of the problem you are having is related to how your data
are arranged in one track, could you send me a set of real data for
one of those tracks rather than a small sample that don't really
represent the problem?

Thanks,
Scott
Hi Scott,
I think I am using Gbrowse2, and I made the configure file based on your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.
However, I am not 100 percent sure of this. Can you tell me how can I check
the version of Gbrowse.
Another point is that, you see, GBrowse2 didn't provide the configure file
of Arabidopsis, so we generated this file by ourselves. However, the file is
made by my colleague, so I am not sure if he took this configure file from
the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is from
GBrowse1.x, I will ask my colleague and make sure of this. Thanks.
Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using?  Your conf
file looks like GBrowse 1.X.  Also, I trimmed the GMOD help desk email
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine.  There is a
problem either with your data, your config or both.  I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal characters.
Scott
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think, would be
the boxes are too close. For example, if the start and end positions are
1    10    0.8    .    .
11    20    0.7    .    .
21    30    0.7    .    .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4    7    0.8    .    .
14    17    0.7    .    .
24    27    0.7    .    .
They would be on the same line. However, in the case of my data, it is hard
to determine what values should be added or subtracted. For example, I used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure all of
the boxes are on the same line for every scale of zooming in or zooming out.
Jiantao Yu
2012-04-27 17:20:28 UTC
Permalink
Hi Scott,

I have sent the data to your email box.

Jiantao
Post by Scott Cain
Hi Jiantao,
The easiest way to tell what version of GBrowse you are using is the
location of the config files: if they are int /etc/gbrowse, it's
GBrowse2. If not, it's probably GBrowse 1.
Since part of the problem you are having is related to how your data
are arranged in one track, could you send me a set of real data for
one of those tracks rather than a small sample that don't really
represent the problem?
Thanks,
Scott
Hi Scott,
I think I am using Gbrowse2, and I made the configure file based on your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.
However, I am not 100 percent sure of this. Can you tell me how can I
check
the version of Gbrowse.
Another point is that, you see, GBrowse2 didn't provide the configure
file
of Arabidopsis, so we generated this file by ourselves. However, the
file is
made by my colleague, so I am not sure if he took this configure file
from
the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is from
GBrowse1.x, I will ask my colleague and make sure of this. Thanks.
Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using? Your conf
file looks like GBrowse 1.X. Also, I trimmed the GMOD help desk email
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine. There is a
problem either with your data, your config or both. I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal
characters.
Post by Scott Cain
Scott
On Fri, Apr 27, 2012 at 12:13 PM, Jiantao Yu <
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think,
would
Post by Scott Cain
be
the boxes are too close. For example, if the start and end positions
are
Post by Scott Cain
1 10 0.8 . .
11 20 0.7 . .
21 30 0.7 . .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4 7 0.8 . .
14 17 0.7 . .
24 27 0.7 . .
They would be on the same line. However, in the case of my data, it is hard
to determine what values should be added or subtracted. For example, I used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure all of
the boxes are on the same line for every scale of zooming in or
zooming
Post by Scott Cain
out.
Scott Cain
2012-04-27 21:58:40 UTC
Permalink
Hi Jiantao,

I managed to reproduce your problem. It turns out that "group on =
source" doesn't appear to work with the current bioperl. I fixed it
for the sample data you gave me (for Chr1 only, and one source only),
by adding to each line a "Name=fake;" and then changing the config to
do "group on = display_name". So, for example, one line of the GFF
would look like this:

Chr1 MSH1_dr_vs_Col_0 meylaSW_MSH1_1000K_feature 475006 524995
0.777166 . . Name=fake;Note=Wi..

Scott
Hi Scott,
I think I am using Gbrowse2, and I made the configure file based on your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.
However, I am not 100 percent sure of this. Can you tell me how can I check
the version of Gbrowse.
Another point is that, you see, GBrowse2 didn't provide the configure file
of Arabidopsis, so we generated this file by ourselves. However, the file is
made by my colleague, so I am not sure if he took this configure file from
the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is from
GBrowse1.x, I will ask my colleague and make sure of this. Thanks.
Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using?  Your conf
file looks like GBrowse 1.X.  Also, I trimmed the GMOD help desk email
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine.  There is a
problem either with your data, your config or both.  I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal characters.
Scott
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think, would be
the boxes are too close. For example, if the start and end positions are
1    10    0.8    .    .
11    20    0.7    .    .
21    30    0.7    .    .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4    7    0.8    .    .
14    17    0.7    .    .
24    27    0.7    .    .
They would be on the same line. However, in the case of my data, it is hard
to determine what values should be added or subtracted. For example, I used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure all of
the boxes are on the same line for every scale of zooming in or zooming out.
Jiantao Yu
2012-04-27 23:53:34 UTC
Permalink
Hi Scott,

Many thanks for your help! It has been successful!! Could you please tell
me the reason why we can give the same name to many entries, however,
shouldn't give the same IDs to many entries. Except the reason you said
that a big bulk of data will belong to one feature in this case, is there
any other reason for not doing this? I am not sure why the performance will
become poor?

By the way, in the case of my data, I want to group one kind of name, fake,
into subtrack, and group another kind of name, fake2, into another
subtrack, and give them different colors to display. I used this script,
but it looked useless. Could you please help me again? thanks for your
patience.

[solveScatter3]
feature = scatter_feature3
glyph = xyplot
graph_type = boxes
subtrack select = Strand strand
subtrack table = :OverMethy +1 ;
:UnderMethy -1
subtrack select fgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
subtrack select bgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
label = 0
height = 80
min_score = 0
max_score = 205
scale = none
group_on = display_name
category = Quantitative Data
key = solveScatter3

The last question is, why can 'scale' NOT be set up as 'left' or 'right',
or else, there are many scale-coordinates (y-axis) appearing in the screen?

Thanks again.

Jiantao
Post by Scott Cain
Hi Jiantao,
I managed to reproduce your problem. It turns out that "group on =
source" doesn't appear to work with the current bioperl. I fixed it
for the sample data you gave me (for Chr1 only, and one source only),
by adding to each line a "Name=fake;" and then changing the config to
do "group on = display_name". So, for example, one line of the GFF
Chr1 MSH1_dr_vs_Col_0 meylaSW_MSH1_1000K_feature 475006 524995
0.777166 . . Name=fake;Note=Wi..
Scott
Hi Scott,
I think I am using Gbrowse2, and I made the configure file based on your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.
However, I am not 100 percent sure of this. Can you tell me how can I
check
the version of Gbrowse.
Another point is that, you see, GBrowse2 didn't provide the configure
file
of Arabidopsis, so we generated this file by ourselves. However, the
file is
made by my colleague, so I am not sure if he took this configure file
from
the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is from
GBrowse1.x, I will ask my colleague and make sure of this. Thanks.
Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using? Your conf
file looks like GBrowse 1.X. Also, I trimmed the GMOD help desk email
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine. There is a
problem either with your data, your config or both. I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal
characters.
Post by Scott Cain
Scott
On Fri, Apr 27, 2012 at 12:13 PM, Jiantao Yu <
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think,
would
Post by Scott Cain
be
the boxes are too close. For example, if the start and end positions
are
Post by Scott Cain
1 10 0.8 . .
11 20 0.7 . .
21 30 0.7 . .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4 7 0.8 . .
14 17 0.7 . .
24 27 0.7 . .
They would be on the same line. However, in the case of my data, it is hard
to determine what values should be added or subtracted. For example, I used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure all of
the boxes are on the same line for every scale of zooming in or
zooming
Post by Scott Cain
out.
Jiantao Yu
2015-05-11 16:22:22 UTC
Permalink
Hi Scott

I got the error as following, when I tried to install GBrowser via:

Could not find apache executable on this system. Can't figure out
version number for config file. at
/home/jiantao/GBrowse/install_util/GBrowseInstall.pm line 932.


I tried to solve this problem by
http://sourceforge.net/p/gmod/mailman/message/29595042/

but it didn't help. Can you help me? Thanks!

Jiantao
Hi Scott,
Many thanks for your help! It has been successful!! Could you please tell
me the reason why we can give the same name to many entries, however,
shouldn't give the same IDs to many entries. Except the reason you said
that a big bulk of data will belong to one feature in this case, is there
any other reason for not doing this? I am not sure why the performance will
become poor?
By the way, in the case of my data, I want to group one kind of name,
fake, into subtrack, and group another kind of name, fake2, into another
subtrack, and give them different colors to display. I used this script,
but it looked useless. Could you please help me again? thanks for your
patience.
[solveScatter3]
feature = scatter_feature3
glyph = xyplot
graph_type = boxes
subtrack select = Strand strand
subtrack table = :OverMethy +1 ;
:UnderMethy -1
subtrack select fgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
subtrack select bgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
label = 0
height = 80
min_score = 0
max_score = 205
scale = none
group_on = display_name
category = Quantitative Data
key = solveScatter3
The last question is, why can 'scale' NOT be set up as 'left' or 'right',
or else, there are many scale-coordinates (y-axis) appearing in the screen?
Thanks again.
Jiantao
Post by Scott Cain
Hi Jiantao,
I managed to reproduce your problem. It turns out that "group on =
source" doesn't appear to work with the current bioperl. I fixed it
for the sample data you gave me (for Chr1 only, and one source only),
by adding to each line a "Name=fake;" and then changing the config to
do "group on = display_name". So, for example, one line of the GFF
Chr1 MSH1_dr_vs_Col_0 meylaSW_MSH1_1000K_feature 475006 524995
0.777166 . . Name=fake;Note=Wi..
Scott
Hi Scott,
I think I am using Gbrowse2, and I made the configure file based on your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.
However, I am not 100 percent sure of this. Can you tell me how can I
check
the version of Gbrowse.
Another point is that, you see, GBrowse2 didn't provide the configure
file
of Arabidopsis, so we generated this file by ourselves. However, the
file is
made by my colleague, so I am not sure if he took this configure file
from
the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is
from
GBrowse1.x, I will ask my colleague and make sure of this. Thanks.
Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using? Your conf
file looks like GBrowse 1.X. Also, I trimmed the GMOD help desk email
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine. There is a
problem either with your data, your config or both. I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal
characters.
Post by Scott Cain
Scott
On Fri, Apr 27, 2012 at 12:13 PM, Jiantao Yu <
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think,
would
Post by Scott Cain
be
the boxes are too close. For example, if the start and end positions
are
Post by Scott Cain
1 10 0.8 . .
11 20 0.7 . .
21 30 0.7 . .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4 7 0.8 . .
14 17 0.7 . .
24 27 0.7 . .
They would be on the same line. However, in the case of my data, it
is
Post by Scott Cain
hard
to determine what values should be added or subtracted. For example,
I
Post by Scott Cain
used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure all of
the boxes are on the same line for every scale of zooming in or
zooming
Post by Scott Cain
out.
From another point, I really hope the width of boxes are still kept
continuous, you see, no gaps.
ii) I tried to gave all of the entries, located in the same
chromosome,
Post by Scott Cain
the
same IDs. This method did solve the problem, i.e. the boxes are
fixed on
Post by Scott Cain
the
same line. However, as you told in the last email, this led to a
problem,
the performance became poor, and the gbrowse couldn't display the
curves
Post by Scott Cain
sometimes, if there were lots of boxes which had the same IDs.
So I think the best way would be, can we find a way to display them
on
Post by Scott Cain
the
same line, while no limitation of their IDs?
iii) The reason that there is no title of some tracks, is not very
clear.
However, when I changed the 'key' with some other words, the title
can
Post by Scott Cain
be
normally displayed. So this has not been a problem now.
Thanks very much for your patience.
Regards
Jiantao
Post by Scott Cain
Jiantao,
Please always respond to the mailing list too (reply-all).
No, you absolutely should not try to group these features by ID.
That
Post by Scott Cain
Post by Scott Cain
will result in the database loader putting all of the features
together into one gigantic object in the database, and your
performance will be very poor (GBrowse may stop rendering those
tracks
Post by Scott Cain
Post by Scott Cain
altogether). I'll try to reproduce your problem now.
Scott
On Tue, Apr 24, 2012 at 12:23 PM, Jiantao Yu
Hi Scott,
I still got the picture like the attahed file, although I changed
group_on=subject. Do you think I need to add 'ID=1' for all of the
entries
in .gff3 file, in order to let them displayed on the single line?
GBrowse may group entries according to their IDs? However, when I
did
Post by Scott Cain
Post by Scott Cain
this,
I can't get the specific balloon for each position/block in the
picture,
you
see, I just got a very general description in the balloon, such as this
position is from 1..30Mbp, which is not what I want to get.
Thanks a lot.
Jiantao
Post by Scott Cain
Hi Jiantao,
"subject" should work for your data. Did you try panning or
zooming
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
to another location to make sure GBrowse wasn't using a cached
image
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
(just reloading isn't enough)?
Scott
On Tue, Apr 24, 2012 at 11:44 AM, Jiantao Yu
Hi Scott,
Really thanks for you quick reply. I tried to change group-on
in
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
the
config
file into
group_on = display_name or
group_on =subject
However, it seems no effect. I have attached the .gff3 and
.conf
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
files,
and
the configure script for the .gff3 data starts at the line of
No.1365.
Could you please have a look at them? Thanks very much.
Best regards
Jiantao
Post by Scott Cain
Hello Jiantao,
What you are seeing is almost always a result of the config
and
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
the
data not matching. I think your "group_on" setting is
incorrect;
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
it
is usually something like "group_on = display_name" or
"group_on
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
=
subject". I don't think setting it equal to the name of the
feature
type does anything. If fixing that doesn't work, you could
send
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
a
sample of the GFF to the list. Also, there is a section of
the
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
tutorial that came with GBrowse that covers xyplots that might
help
(look for "quantitative data" in the tutorial).
Scott
On Mon, Apr 23, 2012 at 8:14 PM, Jiantao Yu
Dear Sir/Madam,
I highly appreciate the smart of GBrowse. When I tried to
display
the
quantitative data, and set up the zoom with small values,
such
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
as
40Kbp,
I
got the picture as is attached (picture1.png). However, I
perfer
the
blocks
to locate on the same line, rather than being hierarchical.
I
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
mean,
It
would
be better if the blocks are kept as they are in the zoom of
500Kbp
(all
of
the blocks are at one line, shown in the picture2.png).
Could
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
you
please
tell me how to do this? Many thanks!
[methySW_MSH1_1000K]
feature = methySW_MSH1_1000K
glyph = xyplot
graph_type = boxes
fgcolor = red
bgcolor = red
height = 80
min_score = 0
max_score = 1
scale = none
group_on = methySW_MSH1_1000K
category = Quantitative Data
label = 0
key = Methylation Profile - MSH1_dr_vs_Col0
(Sliding
Windows:1000K-size)
Best wishes,
Jiantao
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
Post by Scott Cain
Post by Scott Cain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Post by Scott Cain
Post by Scott Cain
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
Hi
Jiantao Yu
2015-05-11 16:23:18 UTC
Permalink
Hi Scott

I got the error as following, when I tried to install GBrowser via:

Could not find apache executable on this system. Can't figure out
version number for config file. at
/home/jiantao/GBrowse/install_util/GBrowseInstall.pm line 932.


I tried to solve this problem by
http://sourceforge.net/p/gmod/mailman/message/29595042/

but it didn't help. Can you help me? Thanks!

Jiantao
Hi Scott
Could not find apache executable on this system. Can't figure out version number for config file. at /home/jiantao/GBrowse/install_util/GBrowseInstall.pm line 932.
I tried to solve this problem by
http://sourceforge.net/p/gmod/mailman/message/29595042/
but it didn't help. Can you help me? Thanks!
Jiantao
Hi Scott,
Many thanks for your help! It has been successful!! Could you please tell
me the reason why we can give the same name to many entries, however,
shouldn't give the same IDs to many entries. Except the reason you said
that a big bulk of data will belong to one feature in this case, is there
any other reason for not doing this? I am not sure why the performance will
become poor?
By the way, in the case of my data, I want to group one kind of name,
fake, into subtrack, and group another kind of name, fake2, into another
subtrack, and give them different colors to display. I used this script,
but it looked useless. Could you please help me again? thanks for your
patience.
[solveScatter3]
feature = scatter_feature3
glyph = xyplot
graph_type = boxes
subtrack select = Strand strand
subtrack table = :OverMethy +1 ;
:UnderMethy -1
subtrack select fgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
subtrack select bgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
label = 0
height = 80
min_score = 0
max_score = 205
scale = none
group_on = display_name
category = Quantitative Data
key = solveScatter3
The last question is, why can 'scale' NOT be set up as 'left' or 'right',
or else, there are many scale-coordinates (y-axis) appearing in the screen?
Thanks again.
Jiantao
Post by Scott Cain
Hi Jiantao,
I managed to reproduce your problem. It turns out that "group on =
source" doesn't appear to work with the current bioperl. I fixed it
for the sample data you gave me (for Chr1 only, and one source only),
by adding to each line a "Name=fake;" and then changing the config to
do "group on = display_name". So, for example, one line of the GFF
Chr1 MSH1_dr_vs_Col_0 meylaSW_MSH1_1000K_feature 475006 524995
0.777166 . . Name=fake;Note=Wi..
Scott
Hi Scott,
I think I am using Gbrowse2, and I made the configure file based on
your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.
However, I am not 100 percent sure of this. Can you tell me how can I
check
the version of Gbrowse.
Another point is that, you see, GBrowse2 didn't provide the configure
file
of Arabidopsis, so we generated this file by ourselves. However, the
file is
made by my colleague, so I am not sure if he took this configure file
from
the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is
from
GBrowse1.x, I will ask my colleague and make sure of this. Thanks.
Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using? Your conf
file looks like GBrowse 1.X. Also, I trimmed the GMOD help desk email
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine. There is a
problem either with your data, your config or both. I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal
characters.
Post by Scott Cain
Scott
On Fri, Apr 27, 2012 at 12:13 PM, Jiantao Yu <
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think,
would
Post by Scott Cain
be
the boxes are too close. For example, if the start and end
positions are
Post by Scott Cain
1 10 0.8 . .
11 20 0.7 . .
21 30 0.7 . .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4 7 0.8 . .
14 17 0.7 . .
24 27 0.7 . .
They would be on the same line. However, in the case of my data, it
is
Post by Scott Cain
hard
to determine what values should be added or subtracted. For
example, I
Post by Scott Cain
used
30 as the value, it wasn't enough, I mean, 30 is not enough to
ensure
Post by Scott Cain
all of
the boxes are on the same line for every scale of zooming in or
zooming
Post by Scott Cain
out.
From another point, I really hope the width of boxes are still kept
continuous, you see, no gaps.
ii) I tried to gave all of the entries, located in the same
chromosome,
Post by Scott Cain
the
same IDs. This method did solve the problem, i.e. the boxes are
fixed on
Post by Scott Cain
the
same line. However, as you told in the last email, this led to a
problem,
the performance became poor, and the gbrowse couldn't display the
curves
Post by Scott Cain
sometimes, if there were lots of boxes which had the same IDs.
So I think the best way would be, can we find a way to display them
on
Post by Scott Cain
the
same line, while no limitation of their IDs?
iii) The reason that there is no title of some tracks, is not very
clear.
However, when I changed the 'key' with some other words, the title
can
Post by Scott Cain
be
normally displayed. So this has not been a problem now.
Thanks very much for your patience.
Regards
Jiantao
Post by Scott Cain
Jiantao,
Please always respond to the mailing list too (reply-all).
No, you absolutely should not try to group these features by ID.
That
Post by Scott Cain
Post by Scott Cain
will result in the database loader putting all of the features
together into one gigantic object in the database, and your
performance will be very poor (GBrowse may stop rendering those
tracks
Post by Scott Cain
Post by Scott Cain
altogether). I'll try to reproduce your problem now.
Scott
On Tue, Apr 24, 2012 at 12:23 PM, Jiantao Yu
Hi Scott,
I still got the picture like the attahed file, although I changed
group_on=subject. Do you think I need to add 'ID=1' for all of
the
Post by Scott Cain
Post by Scott Cain
entries
in .gff3 file, in order to let them displayed on the single line?
GBrowse may group entries according to their IDs? However, when
I did
Post by Scott Cain
Post by Scott Cain
this,
I can't get the specific balloon for each position/block in the
picture,
you
see, I just got a very general description in the balloon, such
as
Post by Scott Cain
Post by Scott Cain
this
position is from 1..30Mbp, which is not what I want to get.
Thanks a lot.
Jiantao
Post by Scott Cain
Hi Jiantao,
"subject" should work for your data. Did you try panning or
zooming
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
to another location to make sure GBrowse wasn't using a cached
image
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
(just reloading isn't enough)?
Scott
On Tue, Apr 24, 2012 at 11:44 AM, Jiantao Yu
Hi Scott,
Really thanks for you quick reply. I tried to change group-on
in
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
the
config
file into
group_on = display_name or
group_on =subject
However, it seems no effect. I have attached the .gff3 and
.conf
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
files,
and
the configure script for the .gff3 data starts at the line of
No.1365.
Could you please have a look at them? Thanks very much.
Best regards
Jiantao
Post by Scott Cain
Hello Jiantao,
What you are seeing is almost always a result of the config
and
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
the
data not matching. I think your "group_on" setting is
incorrect;
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
it
is usually something like "group_on = display_name" or
"group_on
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
=
subject". I don't think setting it equal to the name of the
feature
type does anything. If fixing that doesn't work, you could
send
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
a
sample of the GFF to the list. Also, there is a section of
the
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
tutorial that came with GBrowse that covers xyplots that
might
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
help
(look for "quantitative data" in the tutorial).
Scott
On Mon, Apr 23, 2012 at 8:14 PM, Jiantao Yu
Dear Sir/Madam,
I highly appreciate the smart of GBrowse. When I tried to
display
the
quantitative data, and set up the zoom with small values,
such
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
as
40Kbp,
I
got the picture as is attached (picture1.png). However, I
perfer
the
blocks
to locate on the same line, rather than being
hierarchical. I
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
mean,
It
would
be better if the blocks are kept as they are in the zoom of
500Kbp
(all
of
the blocks are at one line, shown in the picture2.png).
Could
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
you
please
tell me how to do this? Many thanks!
[methySW_MSH1_1000K]
feature = methySW_MSH1_1000K
glyph = xyplot
graph_type = boxes
fgcolor = red
bgcolor = red
height = 80
min_score = 0
max_score = 1
scale = none
group_on = methySW_MSH1_1000K
category = Quantitative Data
label = 0
key = Methylation Profile - MSH1_dr_vs_Col0
(Sliding
Windows:1000K-size)
Best wishes,
Jiantao
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
Post by Scott Cain
Post by Scott Cain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Post by Scott Cain
Post by Scott Cain
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
Post by Scott Cain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
Hi
Scott Cain
2015-05-11 18:03:53 UTC
Permalink
Hi Jiantao,

What OS are you using and where is apache installed?

Scott
Hi Scott
Could not find apache executable on this system. Can't figure out version number for config file. at /home/jiantao/GBrowse/install_util/GBrowseInstall.pm line 932.
I tried to solve this problem by
http://sourceforge.net/p/gmod/mailman/message/29595042/
but it didn't help. Can you help me? Thanks!
Jiantao
Hi Scott
Could not find apache executable on this system. Can't figure out version number for config file. at /home/jiantao/GBrowse/install_util/GBrowseInstall.pm line 932.
I tried to solve this problem by
http://sourceforge.net/p/gmod/mailman/message/29595042/
but it didn't help. Can you help me? Thanks!
Jiantao
Hi Scott,
Many thanks for your help! It has been successful!! Could you please
tell me the reason why we can give the same name to many entries, however,
shouldn't give the same IDs to many entries. Except the reason you said
that a big bulk of data will belong to one feature in this case, is there
any other reason for not doing this? I am not sure why the performance will
become poor?
By the way, in the case of my data, I want to group one kind of name,
fake, into subtrack, and group another kind of name, fake2, into another
subtrack, and give them different colors to display. I used this script,
but it looked useless. Could you please help me again? thanks for your
patience.
[solveScatter3]
feature = scatter_feature3
glyph = xyplot
graph_type = boxes
subtrack select = Strand strand
subtrack table = :OverMethy +1 ;
:UnderMethy -1
subtrack select fgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
subtrack select bgcolor = sub {
my $f = shift;
my ($name) = $f->attributes('Name');
return "hotpink" if($name =~ /fake/);
return "blue" if($name =~ /fake1/);
}
label = 0
height = 80
min_score = 0
max_score = 205
scale = none
group_on = display_name
category = Quantitative Data
key = solveScatter3
The last question is, why can 'scale' NOT be set up as 'left' or
'right', or else, there are many scale-coordinates (y-axis) appearing in
the screen?
Thanks again.
Jiantao
Post by Scott Cain
Hi Jiantao,
I managed to reproduce your problem. It turns out that "group on =
source" doesn't appear to work with the current bioperl. I fixed it
for the sample data you gave me (for Chr1 only, and one source only),
by adding to each line a "Name=fake;" and then changing the config to
do "group on = display_name". So, for example, one line of the GFF
Chr1 MSH1_dr_vs_Col_0 meylaSW_MSH1_1000K_feature 475006 524995
0.777166 . . Name=fake;Note=Wi..
Scott
On Fri, Apr 27, 2012 at 12:51 PM, Jiantao Yu <
Hi Scott,
I think I am using Gbrowse2, and I made the configure file based on
your
instruction file, Generic Genome Browser Version 2: A Tutorial for
Administrators.
However, I am not 100 percent sure of this. Can you tell me how can I
check
the version of Gbrowse.
Another point is that, you see, GBrowse2 didn't provide the configure
file
of Arabidopsis, so we generated this file by ourselves. However, the
file is
made by my colleague, so I am not sure if he took this configure file
from
the GBrowse1.x or Gbrowse2.x . If you are sure the configure file is
from
GBrowse1.x, I will ask my colleague and make sure of this. Thanks.
Jiantao
Post by Scott Cain
Hi Jiantao,
I forgot to ask--what version of GBrowse are you using? Your conf
file looks like GBrowse 1.X. Also, I trimmed the GMOD help desk
email
Post by Scott Cain
off the cc list.
For xyplots: having the boundaries agacent shouldn't matter; that is
what the data in the tutorial are, and it works fine. There is a
problem either with your data, your config or both. I'm working on a
simplified case to see if I can reproduce your problem.
For the key/track title problem, I'm guessing you had illigal
characters.
Post by Scott Cain
Scott
On Fri, Apr 27, 2012 at 12:13 PM, Jiantao Yu <
Hi Scott,
i) The reason that the boxes are displayed in hierarchy, I think,
would
Post by Scott Cain
be
the boxes are too close. For example, if the start and end
positions are
Post by Scott Cain
1 10 0.8 . .
11 20 0.7 . .
21 30 0.7 . .
...
They would probably be in hierarchy when I zoom in. However, if I changed
4 7 0.8 . .
14 17 0.7 . .
24 27 0.7 . .
They would be on the same line. However, in the case of my data,
it is
Post by Scott Cain
hard
to determine what values should be added or subtracted. For
example, I
Post by Scott Cain
used
30 as the value, it wasn't enough, I mean, 30 is not enough to
ensure
Post by Scott Cain
all of
the boxes are on the same line for every scale of zooming in or
zooming
Post by Scott Cain
out.
From another point, I really hope the width of boxes are still kept
continuous, you see, no gaps.
ii) I tried to gave all of the entries, located in the same
chromosome,
Post by Scott Cain
the
same IDs. This method did solve the problem, i.e. the boxes are
fixed on
Post by Scott Cain
the
same line. However, as you told in the last email, this led to a
problem,
the performance became poor, and the gbrowse couldn't display the
curves
Post by Scott Cain
sometimes, if there were lots of boxes which had the same IDs.
So I think the best way would be, can we find a way to display
them on
Post by Scott Cain
the
same line, while no limitation of their IDs?
iii) The reason that there is no title of some tracks, is not very
clear.
However, when I changed the 'key' with some other words, the title
can
Post by Scott Cain
be
normally displayed. So this has not been a problem now.
Thanks very much for your patience.
Regards
Jiantao
Post by Scott Cain
Jiantao,
Please always respond to the mailing list too (reply-all).
No, you absolutely should not try to group these features by ID.
That
Post by Scott Cain
Post by Scott Cain
will result in the database loader putting all of the features
together into one gigantic object in the database, and your
performance will be very poor (GBrowse may stop rendering those
tracks
Post by Scott Cain
Post by Scott Cain
altogether). I'll try to reproduce your problem now.
Scott
On Tue, Apr 24, 2012 at 12:23 PM, Jiantao Yu
Hi Scott,
I still got the picture like the attahed file, although I
changed
Post by Scott Cain
Post by Scott Cain
group_on=subject. Do you think I need to add 'ID=1' for all of
the
Post by Scott Cain
Post by Scott Cain
entries
in .gff3 file, in order to let them displayed on the single
line?
Post by Scott Cain
Post by Scott Cain
GBrowse may group entries according to their IDs? However, when
I did
Post by Scott Cain
Post by Scott Cain
this,
I can't get the specific balloon for each position/block in the
picture,
you
see, I just got a very general description in the balloon, such
as
Post by Scott Cain
Post by Scott Cain
this
position is from 1..30Mbp, which is not what I want to get.
Thanks a lot.
Jiantao
Post by Scott Cain
Hi Jiantao,
"subject" should work for your data. Did you try panning or
zooming
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
to another location to make sure GBrowse wasn't using a cached
image
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
(just reloading isn't enough)?
Scott
On Tue, Apr 24, 2012 at 11:44 AM, Jiantao Yu
Hi Scott,
Really thanks for you quick reply. I tried to change
group-on in
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
the
config
file into
group_on = display_name or
group_on =subject
However, it seems no effect. I have attached the .gff3 and
.conf
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
files,
and
the configure script for the .gff3 data starts at the line of
No.1365.
Could you please have a look at them? Thanks very much.
Best regards
Jiantao
Post by Scott Cain
Hello Jiantao,
What you are seeing is almost always a result of the config
and
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
the
data not matching. I think your "group_on" setting is
incorrect;
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
it
is usually something like "group_on = display_name" or
"group_on
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
=
subject". I don't think setting it equal to the name of the
feature
type does anything. If fixing that doesn't work, you could
send
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
a
sample of the GFF to the list. Also, there is a section of
the
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
tutorial that came with GBrowse that covers xyplots that
might
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
help
(look for "quantitative data" in the tutorial).
Scott
On Mon, Apr 23, 2012 at 8:14 PM, Jiantao Yu
Dear Sir/Madam,
I highly appreciate the smart of GBrowse. When I tried to
display
the
quantitative data, and set up the zoom with small values,
such
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
as
40Kbp,
I
got the picture as is attached (picture1.png). However, I
perfer
the
blocks
to locate on the same line, rather than being
hierarchical. I
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
mean,
It
would
be better if the blocks are kept as they are in the zoom
of
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
500Kbp
(all
of
the blocks are at one line, shown in the picture2.png).
Could
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
you
please
tell me how to do this? Many thanks!
[methySW_MSH1_1000K]
feature = methySW_MSH1_1000K
glyph = xyplot
graph_type = boxes
fgcolor = red
bgcolor = red
height = 80
min_score = 0
max_score = 1
scale = none
group_on = methySW_MSH1_1000K
category = Quantitative Data
label = 0
key = Methylation Profile - MSH1_dr_vs_Col0
(Sliding
Windows:1000K-size)
Best wishes,
Jiantao
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott
at
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
scottcain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Post by Scott Cain
Post by Scott Cain
Post by Scott Cain
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
Post by Scott Cain
Post by Scott Cain
dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Post by Scott Cain
Post by Scott Cain
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
Post by Scott Cain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
Hi
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
Jiantao Yu
2012-04-27 16:13:13 UTC
Permalink
Hi Scott,

Thanks for reply. I found some answers for the three questions:
i) The reason that the boxes are displayed in hierarchy, I think, would be
the boxes are too close. For example, if the start and end positions are
like this:

1 10 0.8 . .
11 20 0.7 . .
21 30 0.7 . .
...

They would probably be in hierarchy when I zoom in. However, if I changed
the positions like this (+ or - 4):

4 7 0.8 . .
14 17 0.7 . .
24 27 0.7 . .

They would be on the same line. However, in the case of my data, it is hard
to determine what values should be added or subtracted. For example, I used
30 as the value, it wasn't enough, I mean, 30 is not enough to ensure all
of the boxes are on the same line for every scale of zooming in or zooming
out.
Jiantao Yu
2012-04-24 00:14:37 UTC
Permalink
Dear Sir/Madam,

I highly appreciate the smart of GBrowse. When I tried to display the
quantitative data, and set up the zoom with small values, such as 40Kbp, I
got the picture as is attached (picture1.png). However, I perfer the blocks
to locate on the same line, rather than being hierarchical. I mean, It
would be better if the blocks are kept as they are in the zoom of 500Kbp
(all of the blocks are at one line, shown in the picture2.png). Could you
please tell me how to do this? Many thanks!

BTW: my configure script is like this:

[methySW_MSH1_1000K]
feature = methySW_MSH1_1000K
glyph = xyplot
graph_type = boxes
fgcolor = red
bgcolor = red
height = 80
min_score = 0
max_score = 1
scale = none
group_on = methySW_MSH1_1000K
category = Quantitative Data
label = 0
key = Methylation Profile - MSH1_dr_vs_Col0 (Sliding
Windows:1000K-size)


Best wishes,
Jiantao
Jiantao Yu
2012-04-24 15:44:04 UTC
Permalink
Hi Scott,

Really thanks for you quick reply. I tried to change group-on in the config
file into
group_on = display_name or
group_on =subject

However, it seems no effect. I have attached the .gff3 and .conf files, and
the configure script for the .gff3 data starts at the line of No.1365.

Could you please have a look at them? Thanks very much.

Best regards
Jiantao
Post by Scott Cain
Hello Jiantao,
What you are seeing is almost always a result of the config and the
data not matching. I think your "group_on" setting is incorrect; it
is usually something like "group_on = display_name" or "group_on =
subject". I don't think setting it equal to the name of the feature
type does anything. If fixing that doesn't work, you could send a
sample of the GFF to the list. Also, there is a section of the
tutorial that came with GBrowse that covers xyplots that might help
(look for "quantitative data" in the tutorial).
Scott
Dear Sir/Madam,
I highly appreciate the smart of GBrowse. When I tried to display the
quantitative data, and set up the zoom with small values, such as 40Kbp,
I
got the picture as is attached (picture1.png). However, I perfer the
blocks
to locate on the same line, rather than being hierarchical. I mean, It
would
be better if the blocks are kept as they are in the zoom of 500Kbp (all
of
the blocks are at one line, shown in the picture2.png). Could you please
tell me how to do this? Many thanks!
[methySW_MSH1_1000K]
feature = methySW_MSH1_1000K
glyph = xyplot
graph_type = boxes
fgcolor = red
bgcolor = red
height = 80
min_score = 0
max_score = 1
scale = none
group_on = methySW_MSH1_1000K
category = Quantitative Data
label = 0
key = Methylation Profile - MSH1_dr_vs_Col0 (Sliding
Windows:1000K-size)
Best wishes,
Jiantao
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
Jiantao Yu
2012-04-25 23:35:22 UTC
Permalink
Dear Sir/Madam,

I highly appreciate the smart software, GBrowse2. Could you please tell me
why I can't find the title of the track, when I use gbrowse2 on my-own
data, as is shown in the attached picture. I can see the title of the
tracks and check the their corresponding boxes to select them. However, in
the 'Browser' web-pages, the title of tracks can't be displayed, and there
are two additional triangular buttons to move the genomes which appear
under the above two buttons.

How can I solve this problem? I also found the other tracks I made, expect
this kind of tracks, can be normally displayed. Thanks very much.

Jiantao
Jiantao Yu
2012-04-26 00:58:03 UTC
Permalink
Sorry, the picture is attached now for the question in the last email.

Jiantao
Dear Sir/Madam,
I highly appreciate the smart software, GBrowse2. Could you please tell me
why I can't find the title of the track, when I use gbrowse2 on my-own
data, as is shown in the attached picture. I can see the title of the
tracks and check the their corresponding boxes to select them. However, in
the 'Browser' web-pages, the title of tracks can't be displayed, and there
are two additional triangular buttons to move the genomes which appear
under the above two buttons.
How can I solve this problem? I also found the other tracks I made, expect
this kind of tracks, can be normally displayed. Thanks very much.
Jiantao
Scott Cain
2012-04-27 15:29:51 UTC
Permalink
Hi Jiantao,

I suspect that is a configuration file problem. Can you send it please?

Scott
Post by Jiantao Yu
Sorry, the picture is attached now for the question in the last email.
Jiantao
Dear Sir/Madam,
I highly appreciate the smart software, GBrowse2. Could you please tell me
why I can't find the title of the track, when I use gbrowse2 on my-own data,
as is shown in the attached picture. I can see the title of the tracks and
check the their corresponding boxes to select them. However, in the
'Browser' web-pages, the title of tracks can't be displayed, and there are
two additional triangular buttons to move the genomes which appear under the
above two buttons.
How can I solve this problem? I also found the other tracks I made, expect
this kind of tracks, can be normally displayed. Thanks very much.
Jiantao
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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