Biostar Beta. Not for public use.
How to generate bigwig file from paired end reads that overlap
Entering edit mode
21 months ago
racrna • 0
Aarhus University


I preformed paired end sequencing on an RNA-seq library generated from small RNAs. The 5' ends of R1 and R2 from the pair overlap slightly when mapped. When I convert this to a bigwig file, this creates a bump in the profile as the overlapping portion of the read is counted as two separate reads. Can anyone explain how I can fix this so that overlapping reads are represented as one read in my bigwig file.

Any help much appreciated.


Entering edit mode

What is your duplication rate? I'm asking since you would expect fragments to be randomly distributed over the gene so a overlap should not cause a bump.

Alternatively I'm misunderstanding what you ask - could you post a picture?


Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1