This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Htseq-Count Error: Command Not Found

I was trying to use

htseq-count --mode /home/user/test.sam home/homo_sapiens.GRCh37.70.gtf

I get

htseq-count: Command not found

error.

I have installed the HTSeq package and I am running this command from command line and not in python shell. Can somebody help me with this issue.

Thanks in advance.

htseq sam rna-seq rnaseq
• 8,274 views • link
updated by Biostar Biostar • written by venks venks

1 answer

htseq-count is probably a script that was installed into a location that is has not been added to your path.

find that script and run it directly or via python:

python htseq-count
• 76 views • link
written by Istvan Albert Istvan Albert

Thanks Albert. I still get an error that says "Python: Can't open file 'htseq-count' : [Errno 2] No such file or direcotory " ..

• 199 views • link
written by venks venks

you need to actually find the script and run it from where it is located not just invoke it any place - you also need to learn what it means to run scripts in a command line environment

it will look like:

python /some/place/on/my/computer/htseq-count

and we don't know where it was installed, it should have informed you of it while you installed it

• 39 views • link
written by Istvan Albert Istvan Albert

Thanks. Sorry about that and that works.

• 0 views • link
written by venks venks

also note fomr the htseq-count website, you will need to use at least python 2.5.

Check your python version by typing 

python -V
• 0 views • link
written by Zack • Zack

Log in to answer this question.

More posts like this