gencode_regions

Extract 3'UTR, 5'UTR, CDS, Promoter, Genes from GTF files.

Data

If you only care about the final output, they are hosted build and GTF version wise on riboraptor.

Using Python

Dependencies

We recommend setting up a conda environment with Python>=3 and Python<=3.7 with gffutils v0.9 and pybedtools:

conda create --name gencode_env python=3.7
conda activate gencode_env
conda install -c bioconda gffutils=0.9 pybedtools

Notebooks

• BDGP6
• GRCg6
• GRCz10
• GRCz11
• GRCh38
• MG1655
• GRCm10
• Mmul8
• panTro3
• Rnor6.0
• sacCerR64
• WBcel235
• Felis_catus9.0

The corresponding output gzipped beds are in the data directory.

Using R

Dependencies

• r>=3.2.1
• GenomicFeatures

Run

./create_regions_from_gencode.R <path_to_GFF/GTF> <path_to_output_dir>

Will create exons.bed, 3UTR.bed, 5UTR.bed, genes.bed, cds.bed in <output_dir>

Example

• Download GFF/GTF(GRCh37, v25, comprehensive, CHR) from gencodegenes.org:

   wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz \
   && gunzip gencode.v25.annotation.gff3.gz

• Create regions:

./create_regions_from_gencode.R gencode.v25.annotation.gff3 /path/to/GRCh37/annotation

First exons, Last exons

We use GenePred format to make the process a bit simple.

• Download gtfToGenePred

• Convert gtf to GenePred:

  gtfToGenePred gencode.v25.annotation.gtf gencode.v25.annotation.genepred
  

• Extract first exons:

  python genepred_to_bed.py --first_exon gencode.v25.annotation.genepred
  

• Extract last exons:

  python genepred_to_bed.py --last_exon gencode.v25.annotation.genepred
  

Confused about exons and UTRs?

This should be helpful:

Source: Wikipedia

or probably this:

Source: Biostar