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hisat2_extract_splice_sites.py doesn't work

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?

next-gen rna-seq rna-seq
• 6,024 views • link
written by mahdikhadem95 • mahdikhadem95

Its not hisat2_extract_splice_sites.py; you should use 

extract_splice_sites.py Homo_sapiens.GRCh37.75.gtf > Homo_sapiens_splicesites.txt
• 0 views • link
written by Bioinfonext Bioinfonext

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
• 0 views • link
written by mahdikhadem95 • mahdikhadem95

1 answer

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
• 0 views • link
written by mahdikhadem95 • mahdikhadem95

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