snoGloBe: a box C/D snoRNA interaction predictor

Getting Started

snoGloBe is supported on Linux (tested on Ubuntu, Fedora, CentOS).

Dependencies

snoGloBe works with python 3.5 or greater and requires the following packages available from pip:

pandas
biopython
scikit-learn v0.21.3

snoGloBe also needs

bedtools. Click here for installation guidelines

Installing

First, you must clone the git repository:

cd /path/to/clone/
git clone https://github.com/scottgroup/snoGloBe.git

For easier use, add the /bin/ path of the snoglobe repository to your PATH environment variable. This is easily done by opening your .bashrc file in your $HOME directory and adding this line at the bottom:

export PATH=/path/to/clone/snoglobe/bin:$PATH

You should be able to execute the snoglobe command from your terminal.

snoglobe --help
usage: snoglobe.py [-h] [-v] [-n NB_THREADS] [-s STEPSIZE] [-c CHUNKSIZE]
                   [-t THRESHOLD] [-m] [-w NB_WINDOWS] [--seq] [--verbose]
                   sno_fasta target_ids gtf chromo_fasta_dir output

positional arguments:
  sno_fasta             fasta file containing snoRNA sequences
  target_ids            txt file containing target identifiers (gene_id,
                        transcript_id or exon_id), ids should match the ones
                        in the gtf file
  gtf                   Annotation file in .gtf format. Preferably an
                        annotation of the whole genome or whole chromosomes of
                        specified targets
  chromo_fasta_dir      Directory containing fasta files of individual
                        chromosome
  output                Output file name

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Show the version and exit
  -n NB_THREADS, --nb_threads NB_THREADS
                        Number of threads to be used. Default: 1
  -s STEPSIZE, --stepsize STEPSIZE
                        Number of nucleotides between each target sliding
                        window. Default: 1
  -c CHUNKSIZE, --chunksize CHUNKSIZE
                        Number of combinations to run at once. Default:
                        2500000
  -t THRESHOLD, --threshold THRESHOLD
                        Minimum score for an interaction to be reported, value
                        between 0 and 1. Default: 0.95
  -m, --merge           Use this option to merge consecutive positive windows
                        as one
  -w NB_WINDOWS, --nb_windows NB_WINDOWS
                        Minimum number of consecutive windows for an
                        interaction to be reported. Must be used with -m
                        option. Default: 1
  --seq                 Add target and snoRNA interaction sequences to the
                        output
  --verbose             Print the steps

Recommendation

Running a single snoRNA against every human genes will take a few days. We recommend focusing on a subset of genes of interest and using a cluster for more exhaustive jobs.

Authors

Gabrielle Deschamps-Francoeur
Michelle S Scott - website

Questions should be directed to: gabrielle.deschamps-francoeur@usherbrooke.ca

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

For more information about the GNU General Public License, see http://www.gnu.org/licenses/.

How to cite

Please cite as :

Deschamps-Francoeur G, Couture S, Abou-Elela S, Scott MS. The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets. bioRxiv. 2021. Available from: https://www.biorxiv.org/content/10.1101/2021.09.14.460265v3

scottgroup / snoGloBe

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