hisat2 alignment showing 0% aligned but sam file is 6GB in size.

hisat2 alignment showing 0% aligned but sam file is 6GB in size.

0

Hello,
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?


hisat2


alignment

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