How to find unique mappability regions in the bovine genome?
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5.1 years ago
serpalma.v ▴ 70

From a list of SNPs I want to keep the ones found in unique mappability regions. For human data that is possible to do with the wgEncodeCrgMapabilityAlign100-mer track, but for bovine I cannot find an analogous data base.

If there is such information available for bovine, I would greatly appreciate if someone can point it out. If not, could someone please tell me of an alternative approach?

Thanks in advance

SNP cow Assembly • 1.3k views
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5.1 years ago

If not, could someone please tell me of an alternative approach?

citing http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeMapability

To generate the data, the GEM-mappability program has been employed. The method is equivalent to mapping sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts to produce these tracks) back to the genome using the GEM mapper aligner (up to 2 mismatches were allowed in this case). For each window, a mapability score was computed (S = 1/(number of matches found in the genome): S=1 means one match in the genome, S=0.5 is two matches in the genome, and so on). The CRG Alignability tracks were generated independently of the ENCODE project, in the framework of the GEM (GEnome Multitool) project.

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