Thursday, March 05, 2015

How to extract the gap region in human genome?

Just notice that I should avoid the gap region, esp. when we generate a random background as your null distribution using tools such as bedtools shuffle.

Short answer: go below UCSC Table Browser link and choose to save as a bed file
 http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=allTables&hgta_track=hg19&hgta_table=gap&hgta_regionType=genome&hgta_outputType=primaryTable

As below table shown, 8.28% of hg19 assembly are simply gap.

Gap (gap) Summary Statistics
item count457
item bases239,845,127 (8.28%)
item total239,845,127 (8.28%)
smallest item47
average item524,825
biggest item30,000,000

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2 comments:

  1. de novo sequencing 4:46 AM

    I still couldn't get your idea. Could you explain more? Thanks!



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    1. Xianjun Dong10:33 AM

      If you are not clear why there are gaps in the human genome, you may refer to this post: https://www.biostars.org/p/67068/, or searching "gap region in human genome" in Google.

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