This repository contains the scripts necessary to analyze conservation (PhyloP) scores of alternative splicing (AS) events.
These scripts specifically extract PhyloP scores from intron retention and cassette exon coordinates within the nervous system of the C. elegans roundworm. This code can be adapted for other organisms, organ systems, and alternative splicing types.
Requirements for this pipeline include detailed results from the JUM pipeline (https://github.com/qqwang-berkeley/JUM) as well as BigWig (.bw) files pertaining to your organism of interest. BigWig files can be downloaded from UCSC - in the case of C. elegans, the reference link is as follows: https://hgdownload.cse.ucsc.edu/goldenpath/ce11/phyloP26way/