get coverage of a particular transcript from bedgraph

[manauwer]

i have a bedgraph..

1 0 10540 0
1 10540 10564 4
1 10564 10569 5
1 10569 10590 7
1 10590 10614 3
1 10614 10619 2
1 10619 12045 0

from reads mapped to the genome. now i want to extract a particular transcript
1 925741 944581
from the bedgraph, which would give me only those coordinates and coverage of the transcript provided.

are there any tools to do this job.

i can write perl script to do this, but i have many transcript to find out, please suggest me with a tool, if available.

[sarvidsson]

You can extract the overlapping coverage data with bedtools intersect, e.g.

bedtools intersect -wb -a coverage.bdg -b transcripts.bed

(-wb is helpful to see which transcript in the "b" file overlapped the features in the "a" file - you could add transcript identifiers to the "b" for easier parsing)

But if you are actually interested in the actual number of reads overlapping with transcript features, you're probably better of using the original BAM with a GFF3/GTF file and HTSeq-count (http://www-huber.embl.de/users/ander...doc/count.html) - it has some further interesting features for RNA-Seq (if that's what you're into).