Where Could I Download Mappability Data To Compare My Cnv Calls With?

Question

[Pascal]

Hi. I would like to compare a set of CNV calls I have in BED file format against mappability information. Where could I find this information? (I thought it was available in UCSC track downloads). Thanks.

Answer 1

[Yu]

Yes, there are mapability tracks in UCSC genome browser, named "Mapability" under group "Mapping and Sequencing Tracks" for hg18, hg19, and mm9. You can use Table browser to export the data or download from its FTP site.

[Pascal]

Thanks for your answer. I didn't see "Mappability" track for hg18, but it is indeed available for hg19.

Answer 2

[Fidel]

From the ftp server of USCS you can directly download bigwig mappability files. For mouse the URL is ftp://hgdownload.cse.ucsc.edu/gbdb/mm9/bbi/ Other species are also are available, just browse the different folders.

Answer 3

[Casey Bergman]

The downside of currently available mappability tracks is that there provenance is somewhat unclear. If you want to compute mappability (acutally uniqueness) yourself, see the method described here by Derrien et al.

[Pascal]

Thanks for the paper. Derrien is one the guy who actually produced the Mappability track from CRG institute.

[Fidel]

The mappability tracks found in UCSC are from the CRG using the methods described in the paper that you mention.

[Casey Bergman]

Yes, but not the Duke or DAC tracks, and the exact version of the CRG code used is not specified.