Re: displaying BAM files on JBrowse

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Re: displaying BAM files on JBrowse

Robert Buels-2
On 06/20/2013 11:04 AM, Jayaraman, Pushkala wrote:
 > So how do I display my BAM data? I know I need to use Alignments2 tracks
 > but when I create a separate.conf file how does that configuration pull
 > in the BAM files?
 >
 > Is there another script I need to run?

As Ray said, no scripts, you just add a little snippet of JSON to the
JBrowse configuration (either jbrowse_conf.json or the trackList.json in
your data directory) that points it at the URL of the BAM file.  It
reads it directly.

There's an example configuration on the wiki a little bit down from that
link.

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

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Re: displaying BAM files on JBrowse

Robert Buels-2
Yes, something like that.


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

On 06/20/2013 11:33 AM, Jayaraman, Pushkala wrote:

> Thanks Guys!
> So trackList.json will be my main datasource.config file.. ?
>
>
> {
>           "storeClass"  : "JBrowse/Store/SeqFeature/BAM",
>           "urlTemplate" : "../../raw/volvox/volvox-sorted.bam",
>           "label"       : "volvox-sorted.bam",
>           "type"        : "JBrowse/View/Track/Alignments2",
>           "key"         : "volvox-sorted.bam",
>           "style" : {
>              "className"      : "alignment",
>              "arrowheadClass" : "arrowhead",
>              "labelScale"     : 100
>           }
>        },
>
>
> Is this the configuration you are talking about?