Question: Counting Spliced Pair-End Reads
0
gravatar for Frenkiboy
7.9 years ago by
Frenkiboy250
Frenkiboy250 wrote:

Is there an application that can count the number of overlaps between a BED/GTF file and splice mapped pair-end reads?

(e.g. interval 1 in bed is overlapped by 10 fragments)

Thanks!

rna • 1.5k views
ADD COMMENTlink written 7.9 years ago by Frenkiboy250
1
gravatar for Mikael Huss
7.9 years ago by
Mikael Huss4.7k
Stockholm
Mikael Huss4.7k wrote:

Yes, BEDTools among others. You can use intersectBed and give it a BAM file with alignments (which can be spliced and paired-end) and a BED/GTF file with intervals.

ADD COMMENTlink written 7.9 years ago by Mikael Huss4.7k
0
gravatar for Botond Sipos
7.9 years ago by
Botond Sipos1.7k
United Kingdom
Botond Sipos1.7k wrote:

Check out also the htseq-count tool shipped with the HTSeq Python package.

ADD COMMENTlink written 7.9 years ago by Botond Sipos1.7k
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