ExonGene

Reference-specific analysis and files.

This directory contains gene and exon definitions for builds GRCh37 and GRCH38, based on Ensembl releases 75 and 84, respectively. The workflow here will reproduce these datasets, but that is typically not necessary. In most cases there is nothing to do for this stage.

Key files here are,

• dat/genes.ensXX.bed contains gene definitions
• dat/exons.ensXX.bed contains exon definitions

Development notes

For annotation purposes, we require that gene names match in all genes and exons so they are drawn together. Exons may have optional labels separated by ":" from gene name (see Synthetic branch for details).

Workflow here parses Ensemble GTF file directly to pull out genes and exons. Details of the selection process are in GTFFilter.py. They are ad hoc and vary according to ensembl version. There may be better and more standard ways to obtain gene and exon definitions, which would replace the work here.

We provide a script src/TLAExamine.R (see x.5_examine_GTF.sh) which conveniently examines GTF files by expanding the attributes column into multiple columns. It is useful for debugging and understanding these files better.

2_get_merged_exon_bed.sh and 3_get_gene_bed.sh are production scripts which extract genes and exons from GTF file. These need to be run just once and then the resulting features file can be used for downstream applications.

Steps starting with x are optional or may be necessary only for certain ensembl releases