Hello, so I'm mapping reads from a RNA-seq library to a reference genome using hisat2 with default parameters. Of my total output mapped reads, when checking with samtools flagstat/stats I'm getting a significant amount of secondary alignments (SAM flag 0x100) I've looking on how to deal with these. I have read a good practice article and it says I should keep them, but others keep only uniquely mapped reads and recommend to remove them. Any thoughts? Tools in downstream analysis, for example htseq-count are going to be able to manage them correctly right? I would lose too many reads by removing them, so it is correct if I kept them?
Thank you for time!