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Translate BED Sequences (version 0.2.0)

BED file with added sequence column:

Output from 'Extract Genomic DNA' run on tophat junctions.bed

fasta ID source, e.g. generic:

Any Compomics application such as PeptideShaker, requires a source

fasta ID line separator character:

Only used when a fasta ID source is given, defaults to the pipe character

ID prefix for generated IDs:

Can be used to distinguish samples

Genome reference source:

Genome reference name:

By default, the database metadata will be used.

The SEQTYPE:STATUS to include in the fasta ID lines:

For example: pep:splice

Add the bed score field fasta ID line with this tag name:

For example: with the tag name 'depth' and bed score 12: depth:12

Filter out translations with stop codons before the splice site:

Stop codon filtering start position base pairs:

Do not reject translation is stop_codons are within base pairs of the BED start position for positive strand

Stop codon filtering end position base pairs:

Do not reject translation is stop_codons are within base pairs of the BED end position for negative strand

Trim translations to stop codons:

Minimum length of a translation to be reported:

Translate BED Sequences

This tool takes a BED input file that has been processed by the Galaxy tool "Extract Genomic DNA" to add a 13th column with the transcript sequence.

It generates a peptide fasta file with the 3-frame translations of the spliced sequence defined by each entry in the input BED file.