Counting reads within regions of interest

Question

[EVR]

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

[rania.hamdy1]

I want to count histone modification reads that fall in some predefined regions of a genome using bedtools multicov command i cant understand what BED file refer to How can I know my regions of interest?? on what basis i will create it ? can you help me please?

Answer 1

[Nicolas Rosewick]

-f Minimum overlap required as a fraction of each A. Default is 1E-9 (i.e., 1bp).

Put -f 1

[EVR]

Hi When I put -f 1 it ouptuts counts as 0 for all transcript even though there some reads which lies within the region.

[Nicolas Rosewick]

could you add an iGV screen shot of your region and the bedtools command you used ?

[GenoMax]

Perhaps use coverage instead of multicov?