I need to get all reads that aligned concordantly exactly 1 times base on mpq>40 from hisat2.
samtools view -b -q 40 -o output.bam alignments.bam
Will this command make a job?
I assume "make a job" means "work". Yes, that will work.
Provided samtools was added before view in the command posted :)
yes, sorry, I deleted it accidentally before posting! thanks guys