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

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


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

    1. If you are not clear why there are gaps in the human genome, you may refer to this post:, or searching "gap region in human genome" in Google.