Extract 3'UTR, 5'UTR, CDS, Promoter, Genes from Gencode files

• r>=3.2.1
• GenomicFeatures

./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>

• 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

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
  

This should be helpful:

Source: Wikipedia

or probably this:

Source: Biostar