BioRxiv preprint here.
This repository is for scripts to generate the figures. Bam files are too large to host here, but it is possible to download the fastqs from GEO/SRA and rerun alignment using STAR. Alternatively, run_full_analysis.sh provides a wrapper script to generate plots from saved results (requires all R packages and gtf files for mouse and human).
Please see R package DEQ to run DESeq2, edgeR, and QNB from input and IP bam files as described in our paper.