Counting reads within regions of interest
Hi,
I have a bam and a bed file which has my regions of interest. Now I have would like count all the reads strictly between my regions of interest in bed file. I tried bedtools multicov but it reports the reads which partially overlapped outside regions. I need the count of reads which is confined within my region of interest in bed file.
How can I achieve that. thanks in advance
1 answer
-f Minimum overlap required as a fraction of each A. Default is 1E-9 (i.e., 1bp).
Put -f 1
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Nicolas Rosewick
could you add an iGV screen shot of your region and the bedtools command you used ?
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Nicolas Rosewick
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