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

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

We recommend setting up aconda environment withPython>=3 andPython<=3.7 withgffutilsv0.9 andpybedtools:

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

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

The corresponding output gzipped beds are in thedata directory.

• r>=3.2.1
• GenomicFeatures

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

Will createexons.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 useGenePred format to make the process a bit simple.

• DownloadgtfToGenePred

• Convert gtf to GenePred:

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

• Extractfirst exons:

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

• Extractlast exons:

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

This should be helpful:

Source: Wikipedia

or probably this:

Source: Biostar