Downloading data from UCSC table browser

UCSC table browser is a great tool that can be used to download different annotation data such as exon, intron, 5’ UTR, 3’ UTR etc.

Here is an example to extract the exons from human genome version hg19:

• Select genome to Human
• Select group as Genes and Predictions
• Select your desired track. I have chosen GENCODE V41lift37.
• Select region to position if you have specific region of interest else, keep it at genome.
• Select output format as BED. This will generate output in bed format with each row representing as one exonic region.
• Give your output file name
• Select the output file type and then click get output. This will open another window, where you can select which genome region you want to extract. Look at the figures below for details.

You can also download the gtf file, and parse the file to get the desired information such as TSS, intergenic region, exons, introns etc. You need to install bedtools for this.

Extracting intergenic region

awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' hg19_gencode.v41lift37.annotation.gtf | sortBed | complementBed -i stdin -g hg19_chrom.sizes > gencode.v41.intergenic_region.bed

Extracting exon coordinates

awk '{OFS="\t"} $3=="exon" {print $1,$4-1,$5}' hg19_gencode.v41lift37.annotation.gtf | sortBed | bedtools merge -i stdin > hg19_gencode_v41_exon.bed

Extracting intron coordinates

awk '{OFS="\t"} $3=="gene" {print $1,$4-1,$5}' hg19_gencode.v41lift37.annotation.gtf | sortBed | bedtools subtract -a stdin -b stdin_test.bed > hg19_gencode_v41_intron.bed

The hg38_chrom.sizes can be downloaded from this link. Or you can generate yourself from the fasta file.

# First create index file using samtools

samtools faidx hg19.fa

# Extract column 1 and 2 from genome index file

cut -f1,2 hg19.fa.fai > hg19_chrom.sizes