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smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
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Translation of ORFs #142

Closed SuiyueWestlake closed 11 months ago

SuiyueWestlake commented 11 months ago

Hi,

I used ribotrice to detect a number of ORFs. And the following step of my research is to translate these ORFs to peptides. So I was wondering if there is a tool that you recommend to further translation based on the output format of ribotrice.

Thank you for your help!

Best, Yue

saketkc commented 11 months ago

You can use the orfs-seq subcommand to generate the corresponding DNA or Protein sequences of the ORFs:

 $ ribotricer orfs-seq --help
Usage: ribotricer orfs-seq [OPTIONS]

  Generate sequence for ORFs in ribotricer's index

Options:
  --ribotricer_index TEXT  Path to the index file of ribotricer This file
                           should be generated using ribotricer prepare-orfs
                           [required]
  --fasta TEXT             Path to FASTA file  [required]
  --protein                Output protein sequence instead of nucleotide
  --saveto TEXT            Path to output file  [required]
  -h, --help               Show this message and exit.