Question: Counting reads within regions of interest
0
gravatar for EVR
3.2 years ago by
EVR540
Earth
EVR540 wrote:

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

rna-seq coverage bam • 1.3k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by EVR540

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?

ADD REPLYlink written 27 days ago by rania.hamdy10
0
gravatar for Nicolas Rosewick
3.2 years ago by
Belgium, Brussels
Nicolas Rosewick7.7k wrote:

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

Put -f 1

ADD COMMENTlink written 3.2 years ago by Nicolas Rosewick7.7k

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

ADD REPLYlink written 3.2 years ago by EVR540

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

ADD REPLYlink written 3.2 years ago by Nicolas Rosewick7.7k

Perhaps use coverage instead of multicov?

ADD REPLYlink written 3.2 years ago by genomax68k
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