RefGeneTxtToBed

Convert UCSC refGene.txt to bed format

Dependency

Python (>= 3.6), bedtools-2.24.0

Get refGene.txt from UCSC

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz

Execute

python ref_seq2bed.py refGene.txt.gz ${Path_to_BEDTools}

Output

refGene.coding.exon.bed
refGene.coding.intron.bed
refGene.coding.5putr.bed
refGene.coding.3putr.bed