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4.4 years ago
MAPK
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2.1k
I have a sorted bam file and a bed file with chromosome regions. I would like to:
- get mean coverage for the regions in my .bed file.
- 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!