TRANSDECODER PREDICT

Predict the likely coding regions from the ORFs identified by Transdecoder.LongOrfs. Optionally include results from homology searches (blast/hmmer results) as ORF retention criteria.

Example

This meta-wrapper can be used in the following way:

rule transdecoder_predict:
    input:
        fasta="test.fa.gz", # required input; optionally gzipped
        pfam_hits="pfam_hits.txt", # optionally retain ORFs with hits by inputting pfam results here (run separately)
        blastp_hits="blastp_hits.txt", # optionally retain ORFs with hits by inputting blastp results here (run separately)
        # you may also want to add your transdecoder longorfs result here - predict will fail if you haven't first run longorfs
        #longorfs="test.fa.transdecoder_dir/longest_orfs.pep"
    output:
        "test.fa.transdecoder.bed",
        "test.fa.transdecoder.cds",
        "test.fa.transdecoder.pep",
        "test.fa.transdecoder.gff3"
    log:
        "logs/transdecoder/test-predict.log"
    params:
        extra=""
    wrapper:
        "0.66.0/bio/transdecoder/predict"

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Authors

    1. Tessa Pierce

Code