Closed:How to properly get BED regions coverage
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4.4 years ago
MAPK ★ 2.1k

I have a sorted bam file and a bed file with chromosome regions. I would like to:

  1. get mean coverage for the regions in my .bed file.
  2. calculate the percentage of these regions covered at 30X, and at 40X

for 1, I tried

coverageBed -abam file.bam  -b region.bed -mean > mean.txt

which gave me a table with multiple columns:

22      17052775        17052926        K00193:107:HFV7CBBXX:6:1228:23054:40666/1       60      +       17052775        17052926        0,0,0   1       151,    0,     
0.0000000 22      17052775        17052926        K00193:107:HFV7CBBXX:6:2228:24718:39822/1       60      +       17052775        17052926        0,0,0   1       151,    0,     
0.0000000 22      17052806        17052957        K00193:107:HFV7CBBXX:6:2126:29183:23540/1       60      +       17052806        17052957        0,0,0   1       151,    0,     
0.0000000

What would be the easiest to get these done? I tried several post on Biostars/google, but couldn't find the solution for these. Any suggestions would be much appreciated!

bedtools • 92 views
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