briscoe-nf-tobias

Analysis pipeline for Joaquinas work with the tobias analysis tool

Pipeline outline

The pipeline runs the different steps of the TOBIAS footprinting tool. For detailed descriptions of each step visit their wiki.

Given a design file, a motif file and mapped files (bam format) it will run TOBIAS' ATACorrect, ScoreBigwig, BINDetect of all against all conditions and it will generate PlotAggregate metaplots of corrected insertions for each motif in the file.

Usage

The release is set to the latest version, to run the development version of the pipeline, change to -r dev

The pipeline can be run as in the following example:

#!/bin/sh

export NXF_WORK="/path/to/work"
export NXF_SINGULARITY_CACHEDIR="/path/to/sing"

## LOAD REQUIRED MODULES
ml purge
ml Nextflow/21.04.0
ml Singularity/3.4.2
ml Graphviz

## UPDATE PIPLINE
nextflow pull luslab/briscoe-nf-tobias

## RUN PIPLINE
nextflow run luslab/briscoe-nf-tobias \
  -r master \
  -profile crick_tobias \
  --genome genome.fa \
  --regions regions.bed \
  --peaks regions.bed \
  --blacklist blacklist.bed \
  --motifs motifs \
  --design design.csv \
  --skip_bam_index true
  

--genome

Path to genome in fasta format used in ATACorrect and BINDetect.

--regions

Path to BED file with the open chromatin regions for these experiment. Used for ATACorrect.

--peaks

Can be the same BED file as --regions or a different BED file of regions of interest. Used for BINDetect.

--blacklist

Path to Blacklisted regions in BED format. Used for ATACorrect

--motifs

Path to Motif file in JASPAR or MEME format.

--design

Csv file with paths and condition grouping with the following header: sample_id,data1,data2

• sample_id correspond to the sample name
• data1 corresponds to the path to the .bam
• data2 corresponds to the path to the .bam.bai, if available

--skip_bam_index

This should be true if you are providing paths to your .bam.bai

--output_peaks (optional)

Provide this parameter as a bed file. From the manual:

  --output-peaks <bed>             Gives the possibility to set the output peak set
                                 differently than the input --peaks. This will limit all
                                 analysis to the regions in --output-peaks. NOTE:
                                 --peaks must still be set to the full peak set!