Question: Creatig TrackHubs from BigWigs
0
gravatar for Dataminer
4.6 years ago by
Dataminer2.6k
Netherlands
Dataminer2.6k wrote:

Hi,

Does anyone has a script, that can be shared to create track hub for a list of files present in a directory and in its sub directories  based upon the genome they belong to. The genome could be hg18, hg19, mm9, mm10 etc. Of course this genome information is already present in the name of bigwigs.

The naming convention that I have used is:

flowcell_lane_id_genome.bw

 

kindly help with a script.

Thank you

 

ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 4.6 years ago by Dataminer2.6k
2
gravatar for Ryan Dale
4.6 years ago by
Ryan Dale4.8k
Bethesda, MD
Ryan Dale4.8k wrote:

I wrote the trackhub package to do exactly this.  It allows you to flexibly configure and upload track hubs to UCSC.  The README has an example that should take minimal editing to work for the use-case you describe.

ADD COMMENTlink written 4.6 years ago by Ryan Dale4.8k
1
gravatar for Pierre Lindenbaum
4.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

I played with TrackHubs last year. See my blog: http://plindenbaum.blogspot.fr/2013/07/playing-with-ucsc-genome-browser-track.html

The script is hosted on github: https://github.com/lindenb/genomehub

 

ADD COMMENTlink written 4.6 years ago by Pierre Lindenbaum119k
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