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Old 01-22-2015, 09:38 PM   #1
manauwer
Junior Member
 
Location: new delhi, india

Join Date: Dec 2014
Posts: 3
Default get coverage of a particular transcript from bedgraph

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.
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