I'm trying to run the python library called how_are_we_stranded_here. I have installed with pip install how_are_we_stranded_here. I have also installed its dependencies i.e kallisto 0.44.0 and RSeQC. On how_are_we_stranded_here's pypi page, it gives the following command under the usage heading:

 check_strandedness --gtf Yeast.gtf --transcripts Yeast_cdna.fasta \
--reads_1 Sample_A_1.fq.gz --reads_2 Sample_A_2.fq.gz

So I tried running the program in the terminal using my own files, the command was:

    check_strandedness --gtf Glycine_max.Glycine_max_v2.1.55.gtf \
--transcripts Glycine_max.Glycine_max_v2.1.cdna.all.fa \
--reads_1 SRR2079644.fastq

But it keeps giving the error

./how_stranded.sh: line 1: check_strandedness: command not found

I will be very thankful for any help on how to run it.

  • 1
    $\begingroup$ You might need to include your pip install output too. The package defines a set of scripts that should get you check_strandedness in your path, and it works for me... so I bet something didn't work right during install. $\endgroup$
    – Jesse
    Dec 10, 2022 at 15:29
  • 1
    $\begingroup$ Would you consider installing this in a conda environment or other virtual environment, to control the background more effectively (with regard to M__'s answer and your comment below). It sounds like there are some issues in the background that might need resolving. $\endgroup$ Dec 13, 2022 at 22:03

1 Answer 1


pip should just work, anyway... Two approaches, point 1 is a last resort approach (not recommended), I definitely recommend point 2.

First try,

python3 -m pip install --upgrade how_are_we_stranded_here

Try again does it work? Error logs?, then possibly ...

  1. You need to find out where it is,
   pip show how_are_we_stranded_here
   pip show check_strandedness
   pip show how_stranded.sh

What you really want is the check_strandedness

cd ~
mkdir bin
./pathtoapp/check_stranded # make sure it works
ln -si /pathwaytoapp/how_stranded.sh /home/whatever/bin/
ln -si /pathwaytoapp/check_strandedness ~/bin/check_strandedness

Then write

export PATH="/home/whatever/bin:$PATH"

or modify .profile or .bashrc, then

source ~/.bash_profile

Try again ...

  1. It is better to perform a conda installation

Install either,

    conda install -c bioconda how_are_we_stranded_here
    conda create --name stranded
    conda activate stranded
    check_strandedness -h
  • 2
    $\begingroup$ Thank you so much for taking out the time to give such a thorough reply. It definitely solved the check-strandedness issue but opened a plethora of other issues, so I just gave up. $\endgroup$
    – pubsurfted
    Dec 11, 2022 at 17:30
  • 2
    $\begingroup$ No problem @pubsurfted, although this one is not 'solved' upvotes always welcome. $\endgroup$
    – M__
    Dec 11, 2022 at 19:12
  • 1
    $\begingroup$ upvoted. Thank you! $\endgroup$
    – pubsurfted
    Dec 12, 2022 at 4:14

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.