Ucsc Conservation Track

Question

[Radhouane Aniba]

Hello everyone,

I have a bed file containing some genomic features with coordinates

I would like to extract automatically two information concerning the UCSC conservation :

• Conserved bases (coverage basically)
• Number of conserved blocks (corresponding to these bases)

I remember there is a ucsc tool that do that but I lost its name, any idea ?

Thanks

Rad

Answer 1

[Pierre Lindenbaum]

The conservation tracks are stored in a set of bigwig files: http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/phastCons46way/

You can access those data using the "bigwig" binaries from the jkent package: http://hgdownload.cse.ucsc.edu/admin/exe/

[Radhouane Aniba]

Yes Pierre, I am looking actually for these sources, but cannot find source files for consForBed for example which could solve my problem, any idea where to find it ?

[Radhouane Aniba]

got all jkent package and I will compile it, thanks pierre