Question: How to find unique mappability regions in the bovine genome?
1
gravatar for serpalma.v
18 months ago by
serpalma.v20
Germany
serpalma.v20 wrote:

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 • 573 views
ADD COMMENTlink modified 18 months ago by Pierre Lindenbaum118k • written 18 months ago by serpalma.v20
1
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

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.

ADD COMMENTlink written 18 months ago by Pierre Lindenbaum118k
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