Hi! I've been trying to find my answer via Google but came up empty handed.
I need to convert a specific Bowtie command line to it's equivalent/closest match in Hisat2. Yet I can't seem to find the corresponding options flags in Hisat2 which are available in Bowtie. The Bowtie command is the following:
bowtie -p [#CPU'S] -l 50 -n 3 -m 2 -e 120 -a --strata --best --sam [INDEX FILE] $FASTQ_FILE $FASTQ_FLIE.sam >bowtie-$FAST_FILE-out
Now from what I understand, '-e 120' was only used as a black box since without it, results would end up being wrong(I don't know why..).
So.. What is the closest match for this command line in Hisat2? Thank you guys!