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Old 09-26-2017, 02:51 PM   #1
SamH2017
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Location: America

Join Date: Sep 2017
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Unhappy Hisat2: no command found in bash

Hi all,
I'm a complete novice at RNAseq mapping and I am trying to follow this protocol using their data: https://www.nature.com/nprot/journal...t.2016.095.pdf

I have downloaded the appropriate files and unpacked them and copied the relevant files into my working directory (HOME/bin) but when I try to run the first command to map the reads to the genome ($ hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1) bash spits out the following error: -bash: hisat2: command not found

The hisat2 executable file in present in my working directory, so I can't understand why it won't run.
Any advice would be much appreciated as my boss is back next week and I would like to have made some progress by then. I've been struggling with this since yesterday and can't seem to get past it.

Thank you in advance.
Samantha
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Old 09-27-2017, 04:18 AM   #2
GenoMax
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While you would be able to get the command to run by doing
Code:
$ ./hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1 etc
you should spend a bit of time with some unix basics. I recommend this UNIX tutorial.
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Old 09-27-2017, 06:08 PM   #3
SamH2017
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Smile Problem solved! :)

Thank you so much GenoMax!! This advice worked a treat!

I will definitely take the time to learn the basics, and hopefully beyond! Thanks for the tutorial link.
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