Hello,

I've got a large number of fastq files generated from a paired end single cell RNAseq experiment. 

I'm looking to align them back to mm10 using Hisat2, I can do this if I run every pair individually but is there a way to get hisat to do them all with one code one after the other?

I'm relatively new to the ubuntu coding environment so feel free to dumb it down.
Thanks in advance
Try this instead and let us know.

    for f in `ls -1 *_1.fastq.gz | sed 's/_1.fastq.gz//' `
    do
    echo hisat2 -x mm10idx -1 ${f}_1.fastq.gz -2 ${f}_2.fastq.gz -S ${f}.bam
    done

