[Gmod-gbrowse] tracks displayed at wrong positions

Discussion:

Thomas LETELLIER

2015-04-13 16:04:18 UTC

Hi everyone,

I succesfully loaded a GFF3 file in a BioDBGFF database but I get some
issues on GBrowse interface:

My GFF3 file contains contig, BAC and markers. When I search for a
contig with the QuickSearch all is fine, I see the contig, BAC and marker.
But when I search for my marker in the quicksearch, these positions
change and GBrowse displays the wrong area.

For example my marker is localized at position 368 641 and GBrowse
changes it to 434 176 when I click on the "search" button.

Here are the GFF3 lines:

ctg2762 assembly contig 65536 671744 . . .
Sequence "ctg2762"; Name "ctg2762"
ctg2762 FPC BAC 65537 671745 . . . BAC
"146DhC741H22"; Name "146DhC741H22"; Marker_hit "AT6D5365 0 0";
Contig_hit "2762"
ctg2762 FPC marker 368641 368641 . . . marker
"AT6D5365"; Name "AT6D5365"; Contig_hit "ctg2762 - 1" (146DhC741H22)

I checked into the database and my marker positions seem good, it's weird.

Best regards,

Thomas

Timothy Parnell

2015-04-14 18:32:12 UTC

Permalink

Hi Thomas,
I suspect it has something to do with the fact that your reference contig starts at 65536 and not at position 1, which is the conventional starting position for most reference sequences in a genome. It is apparently compensating for this (didn’t know it could do this).

Also, if you’re working with GFF3 files, you may want to consider switching to Bio::DB::SeqFeature::Store, which has better native support for GFF3 and is generally faster than the much older Bio::DB::GFF adaptor. Not sure if it would help with the compensating positions, however.

Tim

Post by Thomas LETELLIER
Hi everyone,
I succesfully loaded a GFF3 file in a BioDBGFF database but I get some
My GFF3 file contains contig, BAC and markers. When I search for a
contig with the QuickSearch all is fine, I see the contig, BAC and marker.
But when I search for my marker in the quicksearch, these positions
change and GBrowse displays the wrong area.
For example my marker is localized at position 368 641 and GBrowse
changes it to 434 176 when I click on the "search" button.
ctg2762 assembly contig 65536 671744 . . .
Sequence "ctg2762"; Name "ctg2762"
ctg2762 FPC BAC 65537 671745 . . . BAC
"146DhC741H22"; Name "146DhC741H22"; Marker_hit "AT6D5365 0 0";
Contig_hit "2762"
ctg2762 FPC marker 368641 368641 . . . marker
"AT6D5365"; Name "AT6D5365"; Contig_hit "ctg2762 - 1" (146DhC741H22)
I checked into the database and my marker positions seem good, it's weird.
Best regards,
Thomas
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Scott Cain

2015-04-14 19:03:32 UTC

Permalink

Hi Tim,

I think you are likely right on with the reference sequence problem--the
starting coordinate needs to start with 1.

Also, Thomas said he was working with GFF3 but the sample data he posted is
GFF2, so he probably really has GFF2, and so is using the right database
for it, Bio::DB::GFF.

Scott

On Tue, Apr 14, 2015 at 2:32 PM, Timothy Parnell <

Post by Timothy Parnell
Hi Thomas,
I suspect it has something to do with the fact that your reference contig
starts at 65536 and not at position 1, which is the conventional starting
position for most reference sequences in a genome. It is apparently
compensating for this (didnât know it could do this).
Also, if youâre working with GFF3 files, you may want to consider
switching to Bio::DB::SeqFeature::Store, which has better native support
for GFF3 and is generally faster than the much older Bio::DB::GFF adaptor.
Not sure if it would help with the compensating positions, however.
Tim

On Apr 13, 2015, at 10:04 AM, Thomas LETELLIER <
Hi everyone,
I succesfully loaded a GFF3 file in a BioDBGFF database but I get some
My GFF3 file contains contig, BAC and markers. When I search for a
contig with the QuickSearch all is fine, I see the contig, BAC and

marker.

But when I search for my marker in the quicksearch, these positions
change and GBrowse displays the wrong area.
For example my marker is localized at position 368 641 and GBrowse
changes it to 434 176 when I click on the "search" button.
ctg2762 assembly contig 65536 671744 . . .
Sequence "ctg2762"; Name "ctg2762"
ctg2762 FPC BAC 65537 671745 . . . BAC
"146DhC741H22"; Name "146DhC741H22"; Marker_hit "AT6D5365 0 0";
Contig_hit "2762"
ctg2762 FPC marker 368641 368641 . . . marker
"AT6D5365"; Name "AT6D5365"; Contig_hit "ctg2762 - 1" (146DhC741H22)
I checked into the database and my marker positions seem good, it's

weird.

Best regards,
Thomas

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--
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net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Timothy Parnell

2015-04-14 19:18:25 UTC

Permalink

Ah, you’re right about the GFF version. Thanks for catching that, Scott.

On Apr 14, 2015, at 1:03 PM, Scott Cain <***@scottcain.net<mailto:***@scottcain.net>> wrote:

Hi Tim,

I think you are likely right on with the reference sequence problem--the starting coordinate needs to start with 1.

Also, Thomas said he was working with GFF3 but the sample data he posted is GFF2, so he probably really has GFF2, and so is using the right database for it, Bio::DB::GFF.

Scott

On Tue, Apr 14, 2015 at 2:32 PM, Timothy Parnell <***@hci.utah.edu<mailto:***@hci.utah.edu>> wrote:
Hi Thomas,
I suspect it has something to do with the fact that your reference contig starts at 65536 and not at position 1, which is the conventional starting position for most reference sequences in a genome. It is apparently compensating for this (didn’t know it could do this).

Also, if you’re working with GFF3 files, you may want to consider switching to Bio::DB::SeqFeature::Store, which has better native support for GFF3 and is generally faster than the much older Bio::DB::GFF adaptor. Not sure if it would help with the compensating positions, however.

Tim

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GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Thomas LETELLIER

2015-04-15 08:25:53 UTC

Permalink

Hi,

many thanks Scott & Timothy, you were right contigs need to start with
position 1. I corrected all start positions in my GFF file and the issue
disappeared.

Thanks again :)

Best regards,

Thomas

Post by Scott Cain
Hi Tim,
I think you are likely right on with the reference sequence
problem--the starting coordinate needs to start with 1.
Also, Thomas said he was working with GFF3 but the sample data he
posted is GFF2, so he probably really has GFF2, and so is using the
right database for it, Bio::DB::GFF.
Scott
On Tue, Apr 14, 2015 at 2:32 PM, Timothy Parnell
Hi Thomas,
I suspect it has something to do with the fact that your reference
contig starts at 65536 and not at position 1, which is the
conventional starting position for most reference sequences in a
genome. It is apparently compensating for this (didnât know it
could do this).
Also, if youâre working with GFF3 files, you may want to consider
switching to Bio::DB::SeqFeature::Store, which has better native
support for GFF3 and is generally faster than the much older
Bio::DB::GFF adaptor. Not sure if it would help with the
compensating positions, however.
Tim

On Apr 13, 2015, at 10:04 AM, Thomas LETELLIER
Hi everyone,
I succesfully loaded a GFF3 file in a BioDBGFF database but I

get some

My GFF3 file contains contig, BAC and markers. When I search for a
contig with the QuickSearch all is fine, I see the contig, BAC

and marker.

it's weird.

Best regards,
Thomas

------------------------------------------------------------------------------

BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through

live exercises

http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-

event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF

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