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.