documentation.md

bindz-rbp: workflow documentation

This document describes the individual steps of the workflow. For instructions on installation and usage please go here.

Table of Contents

• Description of workflow steps
  • Rule graph
  • Config file
  • Snakemake Rules
    • all
    • plot_sequence_logos
    • prepare_MotEvo_parameters
    • prepare_sequence_for_MotEvo
    • run_MotEvo_analysis
    • combine_MotEvo_results
    • plot_heatmap_of_MotEvo_results
    • prepare_output_bedfile

Description of workflow steps

Rule graph

Visual representation of workflow. Automatically prepared with Snakemake.

Config file

This workflow requires a config file as in config.yml

Parameter name	Description	Data type(s)
pipeline_path	Absolute path to the pipeline directory	str
seq_name	Input Sequence ID	str
sequence	Input Sequence	str
pwm_directory	Path to the directory with TRANSFAC-formatted PWM files	str
outdir	Path to the output directory	str
MotEvo_bg_binding_prior	MotEvo parameter: prior probability for the background binding	float
MotEvo_min_binding_posterior	MotEvo parameter: prior minimum binding posterior probability	float
MotEvo_Markov_chain_order	MotEvo parameter: order of the Markov chain	float

Snakemake Rules

all

Target rule with final output of the pipeline

• Input
  • A heatmap depicting all the motifs with their sequence logos and names as y-axis tick-labels; input sequence as x-axis; and each cell representing per-position binding probability.
  • BED-formatted list of inferred binding sites.

plot_sequence_logos

Plot sequence logos for the motifs. This rule will run as many times as the number of motifs in the PWM directory.

• Input

  • PWM file containg binding probability matrix
  • Script that generates sequence logos.sequence_logos.py

• Parameters

  • Output directory for the logos
  • File path for cluster logs

• Output

  • A png file containing the sequence logo which will be used in the rule plot_heatmap_of_MotEvo_results

prepare_MotEvo_parameters

Prepare text file with parameters for MotEvo runs

• Parameters

  • MotEvo parameters: bg binding probability, min binding posterior, Markov chain order
  • File path for cluster logs

• Output

  • A text file containing MotEvo paramaters which will be used in the rule run_MotEvo_analysis

prepare_sequence_for_MotEvo

Create a FASTA-formatted file with the input sequence

• Parameters

  • Input sequence (from the configuration file)
  • Header tag for the sequence (constructed from the configuration file)
  • File path for cluster logs

• Output

  • A fasta file which will be used in the rule run_MotEvo_analysis

run_MotEvo_analysis

Run MotEvo for a given FASTA sequence and a given PWM

• Input

  • MotEvo parameters file generated in rule prepare_MotEvo_parameters
  • Path of the PWM directory containing the binding probability matrices
  • Fasta file generated in the rule prepare_sequence_for_MotEvo

• Parameters

  • Absolute path of MotEvo parameters file generated in rule prepare_MotEvo_parameters
  • Absolute path of FASTA file generated in the rule prepare_sequence_for_MotEvo
  • File path for cluster logs

• Output

  • A directory with files containing binding posterior information which will be used in the rule combine_MotEvo_results

combine_MotEvo_results

Combine all motevo results into one TSV file

• Input

  • A directory with files containing binding posterior information which is generated in run_MotEvo_analysis
  • Script that will combine results into one TSV file combine-motevo-results.py

• Parameters

  • Name of the MotEvo output file which contains posterior sites information
  • File path for cluster logs

• Output

  • A TSV file which gathers information from every analysed PWM.

plot_heatmap_of_MotEvo_results

Plot heatmap from the combined_MotEvo_results.tsv file

• Input

  • A TSV file containing information from every analysed PWM, generated from rule combine_MotEvo_results
  • Script that will plot the heatmap with sequence logos as y axis ticks heatmap.r
  • Sequence logos generated for each motif from the rule plot_sequence_logos

• Parameters

  • Input sequence (from the configuration file)
  • Directory with the all sequence logos
  • File path for cluster logs

• Output

  • A heatmap depicting all the motifs with their sequence logos and names as y-axis tick-labels; input sequence as x-axis; and each cell representing per-position binding probability.

prepare_output_bedfile

Prepare a list of all inferred binding sites in a BED format

• Input

  • A TSV file containing information from every analysed PWM, generated from rule combine_MotEvo_results

• Parameters

  • Input sequence ID (from the configuration file)
  • File path for cluster logs

• Output

  • A list of all inferred binding sites in a BED format