You can construct custom track files with your own procedures and provide
a URL in the genome browser that will use those custom tracks in
a browser view.
1. construct your BAM and bigWig/bigBed files and place them on a WEB server so
they can be accessed via a URL reference
http://genome.ucsc.edu/goldenPath/help/bam.html
http://genome.ucsc.edu/goldenPath/help/bigWig.html
http://genome.ucsc.edu/goldenPath/help/bigBed.html
2. construct a small text file consisting of the 'track' definition lines for
each
BAM/bigWig/bigBed file where the bigDataUrl refers to the files you
constructed
in step 1. Place this small file also on your WEB server so it can be
accessed
via a URL.
http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK
3. publish a URL to the genome browser hgTracks CGI, including the
db=<ucscDatabaseName>
and hgt.customText=<url to your file from step 2>
http://genome.ucsc.edu/goldenPath/help/customTrack.html#ADD_CT
http://genome.ucsc.edu/goldenPath/help/customTrack.html
Your data consumer users only need to know about the URL you publish in step 3.
Access that genome browser URL and the custom tracks will be in that view.
You can also update the data in those tracks merely by refreshing the
contents of your BAM/bigWig/bigBed files at their same URL. You do not
need to change anything else. The system will automatically use the
updated files when next viewed.
--Hiram
Elia Stupka wrote:
> Hello there,
>
> we use quite heavily the viewing of BAM and BIGWIG files located on our web
> servers to create sessions for UCL scientists, and although the greatest part
> of our pipeline for NGS analysis is automated we always end up adding custom
> tracks and saving sessions manually, is there a way to do the process
> automatically, through some form of API?
>
> thank you and best regards,
>
> Elia Stupka
>
>
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