tracks displayed at wrong positions

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tracks displayed at wrong positions

Thomas LETELLIER-2
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

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Re: tracks displayed at wrong positions

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 (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

> On Apr 13, 2015, at 10:04 AM, Thomas LETELLIER <[hidden email]> wrote:
>
> 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
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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Re: tracks displayed at wrong positions

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 <[hidden email]> 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

> On Apr 13, 2015, at 10:04 AM, Thomas LETELLIER <[hidden email]> wrote:
>
> 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
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

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Learn Process modeling best practices with Bonita BPM through live exercises
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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_
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Re: tracks displayed at wrong positions

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


On Apr 14, 2015, at 1:03 PM, Scott Cain <[hidden email]<mailto:[hidden email]>> 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 <[hidden email]<mailto:[hidden email]>> 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

> On Apr 13, 2015, at 10:04 AM, Thomas LETELLIER <[hidden email]<mailto:[hidden email]>> wrote:
>
> 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
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
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Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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_
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Re: tracks displayed at wrong positions

Thomas LETELLIER-2
In reply to this post by Scott Cain
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


On 04/14/2015 09:03 PM, Scott Cain 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 <[hidden email]> 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

> On Apr 13, 2015, at 10:04 AM, Thomas LETELLIER <[hidden email]> wrote:
>
> 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
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
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_
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
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_
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