I’m having an issue with mapping using HISAT2 and Bowtie 2. I am trying to map my genome to a reference genome. Both programs run, but the BAM files only show is QNAME and all the other components of the table are blank. I have already gone through trimming and QC and the quality scores are all above 30.
This is example of an error in mapping stats:
Warning: skipping mate #2 of read ‘V300007992L3C001R0141268281/2’ because it was < 2 characters long Warning: skipping mate #1 of read ‘V300007992L3C001R020207830/1’ because length (1) <= # seed mismatches