PCAWG 3 - Expression counting

This repository contains the scripts used for generating the RNA-Seq expression counts on the normal and extended annotation files. Expression counts were generated on gene and exon level for both library-level and merged alignment files. Both HTSeq and DexSeq counts were generated.

Preparation of annotation files

• run_dexseq_annotation.sh - preparation of annotation file for DexSeq
• run_dexseq_extended_annotation.sh - preparation of extended annotation file for DexSeq

Counting

Counting was performed for both HTSeq and DexSeq tools on gene and exon level. For normal and extended annotation, we also generated per-library counts.