I have paired RNA-seq data with high duplication rate. My reads contain UMI so after aligning with
STAR, I run
umitools dedup with
--paired option. I would expect that the output bam file would have an equal number of read1 and read2 (output of
I'm a bit confused with the results as the number of read1 and read2 are equal before using
umitools but after that they are different.
Could anyone please clarify this to me?
Thank you in advance!