Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Issue with Hisat2 frankenndoc Bioinformatics 9 03-04-2019 06:16 AM
HISAT2 executable Dros Bioinformatics 1 06-03-2017 10:46 AM
HISAT2 2.0.5 update tor General 0 02-14-2017 07:31 AM
RSEM with HISAT2 Sbamo RNA Sequencing 8 01-26-2016 05:19 AM
question about hisat2 zhanghao Bioinformatics 3 11-16-2015 05:29 PM

Thread Tools
Old 03-07-2019, 11:31 AM   #1
Junior Member
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:

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
frankenndoc is offline   Reply With Quote

align, hisat2, parallelization

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:06 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO