I'm doing some ChIP-seq and I merged my reads with new data from a rerun.
While my original reads were around 86bp-long, the reads from the rerun are around 50bp-long.
Since I intend to do peak-calling, I woud like to extend my reads so that everything is the same size.
Some tools like bamCoverage from deeptools extend the reads from the BAM file, which is what I want. However, I would like extended reads also in a BAM format and not in a bigWig format...
Do you guys know any tools/approaches that could allow me to extend my reads after I've mapped them to the genome?
Thanks for your answer, you're right, trimming sounds good.