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
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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