hisat2 alignment showing 0% aligned but sam file is 6GB in size.
I am trying to align my fastq files with the reference genome assembly (MRSA ATCC 33591). The sam file formed is some 5-6 GB in size whereas hisat2 output is showing 0.0% alignment rate.
I am confused why the alignment to reference is zero.
Any suggestions on what I am doing wrong?
• 32 views
Read more here: Source link