I need to run Hisat2 on 36 paired-end files. The files are labelled like:
file1_1.fq
file1_2.fq
file2_1.fq
file2_2.fq
For unpaired reads I would use GNUParallel with hisat2 like:
ls *.fq | parallel "hisat2 --dta -x ~/Databases/grch38_tran/genome_tran -U {} -S {.}sam" &
But since for the pairs Hisat2 expects the two files to be input separately (-1, -2) options I don't know how to proceed. Any ideas?
file1_1.fq
file1_2.fq
file2_1.fq
file2_2.fq
For unpaired reads I would use GNUParallel with hisat2 like:
ls *.fq | parallel "hisat2 --dta -x ~/Databases/grch38_tran/genome_tran -U {} -S {.}sam" &
But since for the pairs Hisat2 expects the two files to be input separately (-1, -2) options I don't know how to proceed. Any ideas?
