Snakemake pipeline post-processing scATAC-seq

A snakemake pipeline to split scATACseq bam by cluster, make bigwig tracks, call peaks and recount

How to make a transcript to gene mapping file

I need a transcript to gene mapping file for Salmon. I am aware of annotation bioconductor packages that can do this job. However, I was working on a species which does not have the annotation in a package format (I am going to use Drosphila as an example for this blog post). I had to go and got the gtf file and made such a file from scratch. Please read the specifications of those two file formats.