Pombe_PROseq

this repository contains scripts used for the alignment and manipulation of precision run on sequencing data.

The scripts contained in the folder ScriptsBooth_et_al_2018 were used in the preparation of a manuscript entitled: "Cdk9 regulates a promoter-proximal checkpoint to modulate RNA Polymerase II elongation rate in fission yeast" (PMID: 29416031).

The files contained in the folder 'ScriptsParua_et_al_2018' were used in the preparation of a manuscript entitled: "A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II".

Almost all of the scripts contained within the ScriptsBooth_et_al_2018 and ScriptsParua_et_al_2018 folders depend on an older version of the BigWig R package (developed by Andre Martins). Since this package does not exist on Andre's github, this version of the package is included in the BigWig_Rpackage folder.

Wave calling scripts were derived from polymerase wave calling scripts located here: https://github.com/dankoc/groHMM

Wave calling scripts depend on a more recent version of the bigWig R package which can be downloaded here: https://github.com/andrelmartins/bigWig