hisat2_extract_splice_sites.py doesn't work

Question

[mahdikhadem95]

Hi everyone. I am new to NGS data analysis. Currently I am trying to analyze my RNA-seq data. I encounter an error when I use hisat2_extract_splice_sites.py. This is my code:

hisat2_extract_splice_sites.py Homo_sapiens.GRCh37.75.gtf > Homo_sapiens_splicesites.txt

and this is the result:

hisat2_extract_splice_sites.py: command not found

I am using python 3.6.3

python3 --version
Python 3.6.3

Does anybody know how can I fix this?

[Bioinfonext]

Its not hisat2_extract_splice_sites.py; you should use

extract_splice_sites.py Homo_sapiens.GRCh37.75.gtf > Homo_sapiens_splicesites.txt

[mahdikhadem95]

I have used this command as well. But the result is the same as before:

extract_splice_sites.py Homo_sapiens.GRCh37.75.gtf > Homo_sapiens_splicesites.txt
extract_splice_sites.py: command not found

Answer 1

[mahdikhadem95]

The problem solved!

First I removed the hisat2. then I reinstalled it with conda and updated hisat2 with the following commands:

conda install -c bioconda hisat2
conda update hisat2

now this code executes without any error.

hisat2_extract_splice_sites.py Homo_sapiens.GRCh37.75.gtf > Homo_sapiens_splicesites.txt