TRANSDECODER LONGORFS

TransDecoder.LongOrfs will identify coding regions within transcript sequences (ORFs) that are at least 100 amino acids long. You can lower this via the ‘-m’ parameter, but know that the rate of false positive ORF predictions increases drastically with shorter minimum length criteria.

Example

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

rule transdecoder_longorfs:
    input:
        fasta="test.fa.gz", # required
        gene_trans_map="test.gtm" # optional gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> )
    output:
        "test.fa.transdecoder_dir/longest_orfs.pep"
    log:
        "logs/transdecoder/test-longorfs.log"
    params:
        extra=""
    wrapper:
        "0.66.0/bio/transdecoder/longorfs"

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