Kaessmannlab Wiki

gtftk is a program that you can use to assess and modify .gtf files (the standard file format for genome annotations).

I have used it to modify my gtf files for use in the STAR alignment program and to generate a reference for the Curio Seeker pipeline.

The gtftk github page [ https://github.com/dputhier/pygtftk ] provides some installation instructions. Although they recommend using conda, my conda build did not work, so I ended up using pip instead:

git clone https://github.com/dputhier/pygtftk.git | cd pygtftk | pip install -r requirements.txt | python setup.py install | pip install pygtftk

and then I used conda to install bedtools:

conda install bioconda::bedtools