[Gmod-gbrowse] allele density

Discussion:

jinal jhaveri

2004-02-05 05:11:37 UTC

<BODY>If I want to display the SNP's density (SNPS/500k), I made a following GFF entry
chr1    example my_frequency    250     250     100     +       .       My_Feature s14
Where I wanted that at position 250 , there are 100 snps in the 500k region around the position 250.
My .conf entry for this looks like following!
[frequencyplot] feature      = my_frequency glyph        = xyplot graph_type    = boxes scale         = right bgcolor       = blue fgcolor       = blue max_score     = 260 height        = 35 key          = SNPs/500k 
But apparently I am not getting the results I want (same as <A href="http://www.hapmap.org/cgi-perl/gbrowse/gbrowse/hapmap?name=Chr11">http://www.hapmap.org/cgi-perl/gbrowse/gbrowse/hapmap?name=Chr11</A>). Is my glyph selection wrong? Can anyone help me with the params?
 
thanks a ton
--Jinal</BODY>

Scott Cain

2004-02-05 14:26:34 UTC

Permalink

Hi Jinal,

I'm not familiar with the hapmap data or conf, but I'll still take a
shot at this: when you say you are not getting the results you where
looking for, you didn't say what you where looking for or what you saw.
I suspect that you need an aggregator to collect all of the my_frequency
features to plot them (I take it that you have several more lines of
this type, right?) If so, they all will need to have the same group
name (ie, My_Feature s14), for a given chromosome/contig. Then you can
add to your conf file:

aggregators = snp_freq{my_frequency}

and change your track conf to:

[frequencyplot]
feature = snp_freq
glyph = xyplot
graph_type = boxes
scale = right
bgcolor = blue
fgcolor = blue
max_score = 260
height = 35
key = SNPs/500k

Note that if you want it in the overview like hapmap, you need to change
the part in the '[]' to [frequencyplot:overview]

Does that help? If not you may also want to take a look at the tutorial
included with gbrowse at http://localhost/gbrowse/tutorial/tutorial.html
where there is a section about quantitative data.

Scott

Post by jinal jhaveri
If I want to display the SNP's density (SNPS/500k), I made a following
GFF entry
chr1 example my_frequency 250 250 100 +
. My_Feature s14
Where I wanted that at position 250 , there are 100 snps in the 500k
region around the position 250.
My .conf entry for this looks like following!
[frequencyplot]
feature = my_frequency
glyph = xyplot
graph_type = boxes
scale = right
bgcolor = blue
fgcolor = blue
max_score = 260
height = 35
key = SNPs/500k
But apparently I am not getting the results I want (same as
http://www.hapmap.org/cgi-perl/gbrowse/gbrowse/hapmap?name=Chr11). Is
my glyph selection wrong? Can anyone help me with the params?
thanks a ton
--Jinal
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email is sponsored by EclipseCon 2004 Premiere Conference on Open
Tools Development and Integration See the breadth of Eclipse activity.
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. ***@cshl.org
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Lincoln Stein

2004-02-06 09:24:27 UTC

Permalink

Hi,

This is the right advice. Jinal, if you still have trouble getting
this work please write back.

Lincoln

Post by Scott Cain
Hi Jinal,
I'm not familiar with the hapmap data or conf, but I'll still take
a shot at this: when you say you are not getting the results you
where looking for, you didn't say what you where looking for or
what you saw. I suspect that you need an aggregator to collect all
of the my_frequency features to plot them (I take it that you have
several more lines of this type, right?) If so, they all will need
to have the same group name (ie, My_Feature s14), for a given
aggregators = snp_freq{my_frequency}
[frequencyplot]
feature = snp_freq
glyph = xyplot
graph_type = boxes
scale = right
bgcolor = blue
fgcolor = blue
max_score = 260
height = 35
key = SNPs/500k
Note that if you want it in the overview like hapmap, you need to
change the part in the '[]' to [frequencyplot:overview]
Does that help? If not you may also want to take a look at the
tutorial included with gbrowse at
http://localhost/gbrowse/tutorial/tutorial.html where there is a
section about quantitative data.
Scott

Post by jinal jhaveri
If I want to display the SNP's density (SNPS/500k), I made a
following GFF entry
chr1 example my_frequency 250 250 100 +
. My_Feature s14
Where I wanted that at position 250 , there are 100 snps in the
500k region around the position 250.
My .conf entry for this looks like following!
[frequencyplot]
feature = my_frequency
glyph = xyplot
graph_type = boxes
scale = right
bgcolor = blue
fgcolor = blue
max_score = 260
height = 35
key = SNPs/500k
But apparently I am not getting the results I want (same as
http://www.hapmap.org/cgi-perl/gbrowse/gbrowse/hapmap?name=Chr11)
. Is my glyph selection wrong? Can anyone help me with the params?
thanks a ton
--Jinal
------------------------------------------------------- The
SF.Net email is sponsored by EclipseCon 2004 Premiere Conference
on Open Tools Development and Integration See the breadth of
Eclipse activity. February 3-5 in Anaheim, CA.
http://www.eclipsecon.org/osdn
_______________________________________________ Gmod-gbrowse
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724