Workflow: TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)

Fetched 2022-01-20 14:36:45 GMT
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Inputs

ID Type Title Doc
singleBestOnly Boolean (Optional)
transcriptsFile File [FASTA]

Steps

ID Runs Label Doc
extract_long_orfs
../tools/TransDecoder/TransDecoder.LongOrfs-v5.cwl (CommandLineTool)
TransDecoder.LongOrfs: Perl script, which extracts the long open reading frames

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. TransDecoder identifies likely coding sequences based on the following criteria: + a minimum length open reading frame (ORF) is found in a transcript sequence + a log-likelihood score similar to what is computed by the GeneID software is > 0. + the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 2 forward reading frames. + if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). + a PSSM is built/trained/used to refine the start codon prediction. + optional the putative peptide has a match to a Pfam domain above the noise cutoff score.

Please visit https://github.com/TransDecoder/TransDecoder/wiki for full documentation.

Releases can be downloaded from https://github.com/TransDecoder/TransDecoder/releases

predict_coding_regions
../tools/TransDecoder/TransDecoder.Predict-v5.cwl (CommandLineTool)
TransDecoder.Predict: Perl script, which predicts the likely coding regions

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. TransDecoder identifies likely coding sequences based on the following criteria: + a minimum length open reading frame (ORF) is found in a transcript sequence + a log-likelihood score similar to what is computed by the GeneID software is > 0. + the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 2 forward reading frames. + if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc). + a PSSM is built/trained/used to refine the start codon prediction. + optional the putative peptide has a match to a Pfam domain above the noise cutoff score. Please visit https://github.com/TransDecoder/TransDecoder/wiki for full documentation. Releases can be downloaded from https://github.com/TransDecoder/TransDecoder/releases

Outputs

ID Type Label Doc
coding_regions File
peptide_sequences File
bed_output File
gff3_output File
Permalink: https://w3id.org/cwl/view/git/e9bbe2917384efc75ba067db23612bc8e22f3f06/workflows/TransDecoder-v5-wf-2steps.cwl