/reference-annotations

Makefile for reference annotations for hg19 genes & genomic regions

Primary LanguageMakefile

reference-annotations

Makefile for building .bed formatted reference annotation files for hg19 human genome genes & genomic regions

Usage

First, clone this repository and change to its directory:

git clone https://github.com/stevekm/reference-annotations.git
cd reference-annotations

Generate the desired annotation files from the available entries:

  • all, gencode-hg19, gencode-hg38, ensembl-hg19, ensembl-hg38, ensembl-mm10
make all

# or

make gencode-hg19

# or

make ensembl-hg19

# etc. ....

Output

The following files are created:

  • gencode-hg19: gencode.v19.annotation.genes.bed; Gencode hg19 human gene annotations & genomic regions

  • gencode-hg38: gencode.v27.annotation.genes.bed; Gencode hg38 human gene annotations & genomic regions

  • ensembl-hg19: Homo_sapiens.GRCh37.82.chr.bed; Ensembl hg19 human gene annotations & genomic regions

  • ensembl-hg38: Homo_sapiens.GRCh38.91.chr.bed; Ensembl hg38 human gene annotations & genomic regions

  • ensembl-mm10: Mus_musculus.GRCm38.91.chr.bed; Ensembl mm10 mouse gene annotations & genomic regions

Notes

Intermediate files are removed by default. If you want to keep them, then comment out the .INTERMEDIATE section in the Makefile.

Software

Resources