This repository contains utilities for the generation of gene models and annotations used in the RNA-seq and eQTL pipelines.

Collapsed gene model

Gene-level expression and eQTLs from the GTEx project are calculated based on a collapsed gene model (i.e., combining all isoforms of a gene into a single transcript), according to the following rules:

1. Transcripts annotated as “retained_intron” or “read_through” are excluded. Additionally, transcripts that overlap with annotated read-through transcripts may be blacklisted (blacklists for GENCODE v19, 24 & 25 are provided in this repository; no transcripts were blacklisted for v26).
2. The union of all exon intervals of each gene is calculated.
3. Overlapping intervals between genes are excluded from all genes.

The purpose of step 3 is primarily to exclude overlapping regions from genes annotated on both strands, which can't be unambiguously quantified from unstranded RNA-seq (GTEx samples were sequenced using an unstranded protocol). For stranded protocols, this step can be skipped by adding the --collapse_only flag.

Command:

python3 collapse_annotation.py gencode.v26.GRCh38.annotation.gtf gencode.v26.GRCh38.genes.gtf

where gencode.v26.GRCh38.annotation.gtf is the GTF from GENCODE.

Further documentation is available on the GTEx Portal.