Creatig TrackHubs from BigWigs

Question

[Dataminer]

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

Answer 1

[Ryan Dale]

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.

Answer 2

[Pierre Lindenbaum]

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