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, gencode-hg38v41, 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

• gencode-hg38v41: gencode.v41.annotation.genes.bed; Gencode hg38 human gene annotations version 41 & 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

Annotation Example

In addition to general reference usage, these files can also be used to annotate other genomic region files with a bedmap command like this:

bedmap --echo --echo-map-id --delim '\t' example-NGS-data/ChIP-Seq/bed/Sample1-D-H3K27AC/peaks.bed reference-annotations/gencode.v19.annotation.genes.id4.bed

Notes

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

Software

• GNU make

• bash shell

• BEDOPS

Resources

• Gencode Releases: https://www.gencodegenes.org/releases/

• Ensembl Releases: https://useast.ensembl.org/info/data/ftp/index.html