The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing

This repository contains multiple files related to the manuscript "The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing" (Fowler et al.).

Listed below are the four subdirectories with descriptions of their contents:

Alternative_Splicing_Pipeline - Contains all files and scripts needed to run our alternative splicing identification and annotation software. Requirements include pair-end sequencing runs that are aligned to hg38 or mm10 genomes. There is a separate README for more information on running the pipeline. The following directories need to be unzipped prior to pipeline execution:
/DIPipe/mapability_file_hg19
/DIPipe/mapability_file_hg38
/DIPipe/mapability_file_mm10
/DIPipe/mapability_file_mm
/Genome

Pipeline_Outputs - These are the outputs from the above pipeline we used in our analyses in the manuscript. They include files for quantification using DEXSeq and RSEM for mm10 and hg38 genomes.

Processed_AS_Data - These are the processed and quantified data used in our analyses in the manuscript. These include DEXSeq outputs for mouse and human cells, as well as RSEM outputs for U87 cells.

Scripts - These are shell and R scripts to illustrate how to incorporate the pipeline outputs into the workflow of DEXSeq and RSEM softwares.