I used subread-align to map RNA-seq reads to the reference genome (after index building) resulting in SAM files. Now, I am additionally interested in the unmapped reads (not aligning to the reference), but the subread-package seems to only show the number of unmapped reads and is not collecting them.
1. Is there a way to collect unmapped reads within the subread-package
2. Otherwise, can you suggest a program able to do this?
Thanks a lot