[Gmod-ajax] JBrowse encountered error when displaying bam and vcf

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[Gmod-ajax] JBrowse encountered error when displaying bam and vcf

nikkiborj
Hello to all, I am a new user of JBrowse, I started just last week. I followed the JBrowse Quick-Start Tutorial, I am successful in installing it up to loading my reference sequence and the gff3 feature data file. However, have difficulty displaying my bam and vcf files. The step I've taken is to edit the tracks.conf. 

I apologize, if this is a simple problem. I am quite lost at the moment. Any help would be deeply appreciated.

Thank you very much!

My tracks.conf contains:


[ tracks.rice-bam-track ]

# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.bam
baiUrlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.bai

# settings for how the track looks
category = NGS   #< category for this track
type = JBrowse/View/Track/Alignments2
key  = BAM alignments from rice


[tracks.rice-vcf-track]
label = mysnps
key = SNPs from VCF
storeClass = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz
tbiUrlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz.idx
type = JBrowse/View/Track/HTMLVariants


Below is my JBrowse display:
Inline image 1

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Re: JBrowse encountered error when displaying bam and vcf

Robert Buels-2
The configuration looks OK, it just looks like the .bai file for the BAM
track (and I guess maybe the .idx file for the VCF track?) are not
available on the server.

The first thing I would check for this would be that the .bai file is
actually available at the URL you are giving JBrowse.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 02/03/2014 12:02 AM, Frances Nikki Borja wrote:

> Hello to all, I am a new user of JBrowse, I started just last week. I
> followed the JBrowse Quick-Start Tutorial, I am successful in installing
> it up to loading my reference sequence and the gff3 feature data file.
> However, have difficulty displaying my bam and vcf files. The step I've
> taken is to edit the tracks.conf.
>
> I apologize, if this is a simple problem. I am quite lost at the moment.
> Any help would be deeply appreciated.
>
> Thank you very much!
>
> My tracks.conf contains:
>
>
> [ tracks.rice-bam-track ]
>
> # settings for what data is shown in the track
> storeClass     = JBrowse/Store/SeqFeature/BAM
> urlTemplate    = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.bam
> baiUrlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.bai
>
> # settings for how the track looks
> category = NGS   #< category for this track
> type = JBrowse/View/Track/Alignments2
> key  = BAM alignments from rice
>
>
> [tracks.rice-vcf-track]
> label = mysnps
> key = SNPs from VCF
> storeClass = JBrowse/Store/SeqFeature/VCFTabix
> urlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz
> tbiUrlTemplate =
> /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz.idx
> type = JBrowse/View/Track/HTMLVariants
>
>
> Below is my JBrowse display:
> Inline image 1
>
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: JBrowse encountered error when displaying bam and vcf

Colin Davenport
In reply to this post by nikkiborj
Hi,

first, you shouldn't need to specify the .bam.bai if it's in the same location as the BAM (or at least I don't need to).

urlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz
tbiUrlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz.idx   #can leave out

Second, I have only had success reading in VCF and BAM - so external non-json files - using relative paths. Relative meaning relative to your trackList.json as I remember.

You can check in the error message you get (the red track error) if you're getting closer.

For example, my successful json config is something like
         "urlTemplate" : "../../../colin/seq/xxxx/M-K-15_STAR_s_for.bam",


Regards,
Colin




Date: Mon, 3 Feb 2014 16:02:10 +0800
From: [hidden email]
To: [hidden email]
Subject: [Gmod-ajax] JBrowse encountered error when displaying bam and vcf

Hello to all, I am a new user of JBrowse, I started just last week. I followed the JBrowse Quick-Start Tutorial, I am successful in installing it up to loading my reference sequence and the gff3 feature data file. However, have difficulty displaying my bam and vcf files. The step I've taken is to edit the tracks.conf. 

I apologize, if this is a simple problem. I am quite lost at the moment. Any help would be deeply appreciated.

Thank you very much!

My tracks.conf contains:


[ tracks.rice-bam-track ]

# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.bam
baiUrlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.bai

# settings for how the track looks
category = NGS   #< category for this track
type = JBrowse/View/Track/Alignments2
key  = BAM alignments from rice


[tracks.rice-vcf-track]
label = mysnps
key = SNPs from VCF
storeClass = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz
tbiUrlTemplate = /home/fborja/971.1.1120.sorted.fxmt.mkdup.reAln.GATK.vcf.gz.idx
type = JBrowse/View/Track/HTMLVariants


Below is my JBrowse display:
Inline image 1

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