Re: [Gmod-ajax] Problem with BAM .csi index file

[Scott C. <sc...@sc...>]

Yes, exactly.  I downloaded the bam file and found that the reference
sequences are named like 'chr1A', so Colin's suggestion should do the trick.

On Thu, Sep 24, 2020 at 3:52 PM Colin <col...@gm...> wrote:

> As Scott said, timely question. Standardizing the data files ref names is
> normally good but jbrowse does try to smooth over things like chr1 vs 1 but
> doesn't have chr1A vs 1A right now
>
> In JBrowse 1.16.10, you could try putting this in the jbrowse.conf below
> the [GENERAL] tag
>
>
> replaceRefRename = function(ref) { return
> ref.toLowerCase().replace('chr','') }
>
>
> -Colin
>
> On Thu, Sep 24, 2020 at 6:16 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*
>>>
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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
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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