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Old 03-07-2019, 11:31 AM   #1
frankenndoc
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Location: Canada

Join Date: Mar 2019
Posts: 7
Default Parallelising Hisat2

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?

Last edited by frankenndoc; 03-07-2019 at 11:33 AM. Reason: typo
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