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Re: [Gmod-ajax] Problem with BAM .csi index file
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From: Colin <col...@gm...> - 2020-09-24 23:58:01
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Note also, JBrowse could be programmed to support this out of the box without a custom configuration, we are just trying to help find a solution that works for you, with what we have now :) To see jbrowse's current capabilities for this see https://github.com/GMOD/jbrowse/blob/master/tests/js_tests/spec/RegularizeRefSeqs.spec.js The chr2A/2A does not work but we could add that to our test matrix, etc -Colin On Thu, Sep 24, 2020 at 7:25 PM Colin <col...@gm...> wrote: > While it's nice igv loads it, but they are likely doing similar "smoothing > over" the differences in refname between your bam and the reference genome. > > Most programs do not do any of this smoothing over of this and so it is > generally better to ensure your data is using the same reference sequence > names > > Try: > > samtools view > http://165.227.95.85/jbrowse/data/Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam > 2A > > This fails because your BAM file uses chr2A not 2A. > > As noted above, jbrowse can also try to help this case too, but requires > the replaceRefRename callback > > -Colin > > On Thu, Sep 24, 2020 at 7:03 PM JM C <jua...@gm...> wrote: > >> HI Scott >> >> thank you for your reply. I see your point in there. This shouldn't be >> the case since I'm using the same genome with the same bam file in igv and >> it's working correctly. >> >> This is my track config btw >> >> [ tracks.bam_biointa_2002 ] >> storeClass=JBrowse/Store/SeqFeature/BAM >> >> urlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam >> category=BAM >> type=Alignments2 >> key=Biointa 2002 >> >> csiUrlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam.csi >> >> >> >> >> -- >> *Juan Manuel Crescente* >> >> This message is confidential. You may not copy this message or disclose >> its contents to anyone. >> Please consider the environment before printing this email. >> >> >> On Thu, Sep 24, 2020 at 7:10 PM Scott Cain <sc...@sc...> wrote: >> >>> Hi Juan, >>> >>> Almost always, when this happens, it's because the name of the reference >>> sequence in the BAM file is different from the names of the reference >>> sequences in the seq/refSeqs.json file. If that's the case and you have >>> the very fresh 1.16.10 release, you can use the customRefRename and >>> replaceRefRename options described here: >>> https://jbrowse.org/docs/global_options.html. If you need to go down >>> that path, and enlightenment doesn't immediately strike you, please feel >>> free to write back to this list. >>> >>> Scott >>> >>> >>> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote: >>> >>>> Hi, >>>> >>>> I'm setting up a demo jbrowse with a bam file with .csi index. >>>> >>>> >>>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight= >>>> >>>> I can see the track and got no errors but the track is empty in the >>>> browser. Not sure how to troubleshoot this, any suggestions? >>>> >>>> >>>> -- >>>> *Juan Manuel Crescente* >>>> >>>> This message is confidential. You may not copy this message or disclose >>>> its contents to anyone. >>>> Please consider the environment before printing this email. >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
