Identifying long stretches of Ns in hg19
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addyS • 0
@addys-11305
Last seen 3.9 years ago

Is there a R package to identify long stretches of gaps (Ns) in human genome (hg19)?

bsgenome.hsapiens.ucsc.hg19 hg19 • 448 views
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Mike Smith ★ 5.1k
@mike-smith
Last seen 10 hours ago
EMBL Heidelberg / de.NBI

The 'masked' versions of the reference genomes (e.g. http://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/) come with a mask that represents the gaps in the assembly.

You haven't said what you're trying to do, but you can get the locations of all the gaps on chromosome 1 by doing something like:

library(BSgenome.Hsapiens.UCSC.hg19.masked)
masks(BSgenome.Hsapiens.UCSC.hg19.masked$chr1)[["AGAPS"]]
NormalIRanges object with 39 ranges and 0 metadata columns:
           start       end     width
       <integer> <integer> <integer>
   [1]         1     10000     10000
   [2]    177418    227417     50000
   [3]    267720    317719     50000
   [4]    471369    521368     50000
   [5]   2634221   2684220     50000
   ...       ...       ...       ...
  [35] 206332222 206482221    150000
  [36] 223747847 223797846     50000
  [37] 235192212 235242211     50000
  [38] 248908211 249058210    150000
  [39] 249240622 249250621     10000
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