Translate transcripts from the input BED file into protein sequences.

The genomic sequence:

• may be supplied in an extra column in the BED input file
• retrieved from a twobit genomic reference file
• retrieved from the Ensembl REST API for Ensembl transcripts

INPUTS

• BED file with at least the standard 12 columns
• Genome reference in twobit format (optional)

OUTPUTS

• FASTA of transcript translations
• BED with the genomic location of the translated protein. The added 13th column contains the protein sequence.

OPTIONS

• Feature translation
  • cDNA - three frame translations of the cDNA sequences with an output for each sequence between STOP codons
  • CDS - three frame translations of CDS (coding sequence defined by thickStart and thickEnd in the BED file)
• Translation filtering
  • can be trimmed to a Methionine start codon
  • can be split into peptides by an enzyme digestion
  • must exceed specified minimum length
• BED Filtering
  • genomic regions
  • ensembl biotype if the BED contains the 20 columns as retrieved from the Ensembl REST API