The BNS (RNA Bind-N-Seq Analysis) pipeline is a set of bioinformatics tools to analyze data from high-throughput sequencing experiments of protein-bound RNAs. The current version includes read splitting, calculation of kmer frequencies and enrichments, QC metrics, production of motif sequence logos, and RNA secondary structure analysis.

References:

• Nicole Lambert, Alex Robertson, Mohini Jangi, Sean McGeary, Phillip A. Sharp, Christopher B. Burge,
  RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins
  Mol Cell. 2014 Jun 5;54(5):887-900
• Nicole J. Lambert,, Alex D. Robertson, Christopher B. Burge,
  RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA-Binding Proteins
  Methods Enzymol. 2015 558:465-93.
• Daniel Dominguez, Peter Freese, Maria S. Alexis, Gene W. Yeo, Brenton R. Graveley, Christopher B. Burge
  Sequence, Structure, and Context Preferences of Human RNA Binding Proteins
  Mol Cell. 2018, Volume 70, Issue 5, p854-867.

• RBNS_pipeline Github page

• Module Name: rbns_pipeline (see the modules page for more information)
• Unusual environment variables set
  • RBNS_HOME  installation directory
  • RBNS_BIN       executable directory
  • RBNS_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cig 3335 ~]$ module load rbns_pipeline
[+] Loading singularity  4.0.3  on cn4274
[+] Loading rbns_pipeline  20240907
[user@cn3335 ~]$ RBNS_main.py -h 
Usage: 3to2 [options] file|dir ...

Options:
  -h, --help            show this help message and exit
  -d, --doctests_only   Fix up doctests only
  -f FIX, --fix=FIX     Each FIX specifies a transformation; default: all
  -j PROCESSES, --processes=PROCESSES
                        Run 3to2 concurrently
  -x NOFIX, --nofix=NOFIX
                        Prevent a fixer from being run.
  -l, --list-fixes      List available transformations (fixes/fix_*.py)
  -v, --verbose         More verbose logging
  -w, --write           Write back modified files
  -n, --nobackups       Don't write backups for modified files.
  --no-diffs            Don't show diffs of the refactoring
[user@cn3335 ~]$ RBNS_kmers_by_position.py -h
Usage: 3to2 [options] file|dir ...

Options:
  -h, --help            show this help message and exit
  -d, --doctests_only   Fix up doctests only
  -f FIX, --fix=FIX     Each FIX specifies a transformation; default: all
  -j PROCESSES, --processes=PROCESSES
                        Run 3to2 concurrently
  -x NOFIX, --nofix=NOFIX
                        Prevent a fixer from being run.
  -l, --list-fixes      List available transformations (fixes/fix_*.py)
  -v, --verbose         More verbose logging
  -w, --write           Write back modified files
  -n, --nobackups       Don't write backups for modified files.
  --no-diffs            Don't show diffs of the refactoring
[user@cn3335 ~]$ RBNS_fold_split_reads.py -h
Usage: 3to2 [options] file|dir ...

Options:
  -h, --help            show this help message and exit
  -d, --doctests_only   Fix up doctests only
  -f FIX, --fix=FIX     Each FIX specifies a transformation; default: all
  -j PROCESSES, --processes=PROCESSES
                        Run 3to2 concurrently
  -x NOFIX, --nofix=NOFIX
                        Prevent a fixer from being run.
  -l, --list-fixes      List available transformations (fixes/fix_*.py)
  -v, --verbose         More verbose logging
  -w, --write           Write back modified files
  -n, --nobackups       Don't write backups for modified files.
  --no-diffs            Don't show diffs of the refactoring
[user@cn3335 ~]$ exit
user@biowulf]$