Problem with GBrowse displaying

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Problem with GBrowse displaying

Jiarui Li
Hi Ata,
   I have a problem with the GBrowse displaying for DNA sequencing reads.
   I am doing the analysis for next-generation sequencing. After alignment of the short reads, I got the bam file which have all the information of reads alignment. But when I used GBrowse to display this bam file, I found that some of the reads did not show in the track. For example, if there were 100 reads covering a site in bam file, maybe the GBrowse only show 90 of them.
   Is there any default filteration for displaying bam file in GBrowse?

Thanks

Jiarui Li

------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Problem with GBrowse displaying

girlwithglasses
Has anyone answered this query?

On Tue, Oct 9, 2012 at 12:43 PM, Jiarui Li <[hidden email]> wrote:

> Hi Ata,
>    I have a problem with the GBrowse displaying for DNA sequencing reads.
>    I am doing the analysis for next-generation sequencing. After alignment of the short reads, I got the bam file which have all the information of reads alignment. But when I used GBrowse to display this bam file, I found that some of the reads did not show in the track. For example, if there were 100 reads covering a site in bam file, maybe the GBrowse only show 90 of them.
>    Is there any default filteration for displaying bam file in GBrowse?
>
> Thanks
>
> Jiarui Li
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



--
Amelia Ireland
GMOD Community Support || http://gmod.org

------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Problem with GBrowse displaying

Timothy Parnell
Hi,

My understanding is there is no filtering, at least with regards to alignment score, etc. Something like that could be useful, but can probably be implemented in a callback. Reads that are not aligned, of course, won't display.

GBrowse does have a feature_limit option that can be set, either in the track stanza or the track defaults. Perhaps increasing this limit might help? I don't know what the default is. The bump and related options also controls how many features are displayed before they become collapsed into one. You can read about these in the GBrowse 2 HowTo on the GMOD wiki.

Does that help?
Tim

On Oct 12, 2012, at 10:32 AM, Amelia Ireland wrote:

> Has anyone answered this query?
>
> On Tue, Oct 9, 2012 at 12:43 PM, Jiarui Li <[hidden email]> wrote:
>> Hi Ata,
>>   I have a problem with the GBrowse displaying for DNA sequencing reads.
>>   I am doing the analysis for next-generation sequencing. After alignment of the short reads, I got the bam file which have all the information of reads alignment. But when I used GBrowse to display this bam file, I found that some of the reads did not show in the track. For example, if there were 100 reads covering a site in bam file, maybe the GBrowse only show 90 of them.
>>   Is there any default filteration for displaying bam file in GBrowse?
>>
>> Thanks
>>
>> Jiarui Li
>>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Amelia Ireland
> GMOD Community Support || http://gmod.org
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse