I recently finished mapping an RNAseq run using STAR2.3.0 and noticed the read1 and read2 counts are different, according to samtools flagstat.
The map% is ~80% but the R1 R2 counts are:
This usually does not happen for PE sequencing, which makes me a bit nervous to proceed with analysis. What are some potential reasons something like this could occur? I do not have experience with this happening and can't seem to find reasons by searching the web.