Annotate counts region by region
Hi guys, I know it could be an answer 1000 times redundant but I looked around without find a quick solution. I have 5 .bam files and a .gtf file that looks like this:
1 134202951 134202953 1 134202954 134203590 1 134199215 134203590
where 1 indicates chromosome 1 and the other two columns respectively start and end position of the chromosome region. I simply would like, for each start-end to have the number of counts. I tried using
overlap.counts1 <- countOverlaps(bedfile,bamfile1)
for a single file but it outputs the total number of counts not region per region. Can anyone help me please?
thank you in advance
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There are several similar threads, maybe one of them has a suitable solution.
Counting Number Of Bam Reads Directly Within Set Of Intervals With Bedtools
How To Calculate The Coverage Of A Specific Interval Based On Data From A Bam File
how to get the coverage for the entire interval
Read depth interval comparison
Also see this function: calculateBamCoverageByInterval().