README.md

Prediction of Trypanosomatid Regulatory Elements

Overview

Features

• Sequence motifs
  • 5' UTR
  • 3' UTR
  • Upstream gene's 3' UTR
  • Downstream genes 5' UTR
  • Upstream intergenic region
  • Downstream intergenic region
  • CDS
• Sequence composition
  • 5' UTR GC/CT composition
  • 3' UTR GC/CT composition
  • CDS GC/CT composition
  • Polypyrimidine tract GC/CT composition
  • Kmer counts
• Sequence lengths
  • 5' UTR length
  • 3' UTR length
  • Polypyrimidine tract length
  • Interenic region / inter-CDS length
• Other
  • CDS codon adaptation index (CAI)

Installation

The Trypanosomatid Regulatory Elements prediction pipeline makes use a number of different R and Python packages, as well as several standalone tools.

Below is a list of all of the requirements needed to run this pipeline.

Requirements

Software requirements

• CMFinder (0.2)
• Infernal (1.1.2+)
• EXTREME (2.0)
• Jellyfish ()

Python requirements

• Python 3
• Snakemake (3.10.0+)
• Biopython (1.6.8+)
• Numpy ()
• Pandas (0.19.2+)
• PyYAML(3.12+)

R requirements

• Bioconductor (3.3+)
• Biostrings (2.40.0+)
• caret (6.0-73+)
• tibble (1.2+)
• seqLogo (1.38+)

conda create -n reg-predict --file requirements.txt \
    --channel bioconda \
    --channel conda-forge \
    --channel pytorch

Note: In order to avoid running out of memory during execution, the hierarchical clustering portion of the EXTREME script run_consensus_clusering_using_wm.pl may need to be edited to increase the value Xmx, e.g.: -Xmx10000m.

Usage

TODO: describe software for predicting UTR boundaries, etc.

snakemake --configfile settings/config.yml combine_motifs