β

To-do for version 2

Include plotting motifs around TSSs on both strands separately to check if a pyrimidine-purine (initiator-like) motif is present on both strands. This lets a user check if TSSs are shifted (are not a pyrimidine-purine pair) and/or initiator motifs are different on the two strands (neither should happen).
Track generation for the genome browser (normalized counts).
Investigate and ideally resolve the issue with CAGEr using only one thread when reading samples and working within the pipeline. Get in touch with Charles Plessy after a reasonable investigation. (Damir discovered that CAGEr uses the number of thread equal to the number of read input files, independently of the number of threads set to it; but it is still unclear why CAGEr uses only one thread for multiple input samples when run within the pipeline.)

Cite in CITATIONS.md all the tools that we used.
Make it possible to run the pipeline by providing the GitHub repository name (and, possibly, a version name / commit hash), instead of making the user clone the repository first.