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

(if you do not have BEDOPS installed and in your PATH you can also run the make bin recipe to download it in the current dir)

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