bam2peaks -nf

Nextflow pipeline for peaks calling with MACS

Description

Nextflow pipeline designed for peak calling using MACS and IDR, coupled with QC generation using deeptools. The saturation option generates peaks by successively considering increasing percentages of the total reads, repeating the operation multiple times within the range of 0.05 to 0.95.

Dependencies

1. Nextflow : for common installation procedures see the IARC-nf repository.

MACS

2. MACS2 or MACS3

IDR (Irreproducible Discovery Rate)

3. IDR

Deeptools

4. Deeptools

A conda receipe, and docker and singularity containers are available with all the tools needed to run the pipeline (see "Usage")

Input

Type	Description
--input_file	input tabulation-separated values file with columns sample (sample name), tag (short name for figures), bam (bam file path) and group (group), for chip mode, you must also provide input : 0 for normal samples and 1 for input sample

eg:

sample	tag	bam	group	input
SAM015	S15	S15.bam	1	0
SAM016	S16	S16.bam	1	0
SAM010	S10	S10.bam	1	1

Parameters

• Mandatory

Name	Example value	Description
--ref	hg38	Reference fasta file hg19, hg38 or mm10'
--gencode	gencode.bed	gencode file

• Optional

Name	Default value	Description
--mode	atac	There is two mode : atac or chip, chip require "input" sample(s)
--output_folder	bam2peaks	Output folder name
--cpu	16	number of CPUs
--mem	16	memory
--extsize	150	MACS extsize : extendsize of peaks to to fix-sized fragments.

• Flags

Flags are special parameters without value.

Name	Description
--help	print usage and optional parameters
--broad	Compute broadpeaks instead of narrowpeaks
--ignoreDuplicates	Ignore duplicates reads
--saturation	Run saturation process

Usage

To run the pipeline for ATAC, one can type:

nextflow run iarcbioinfo/bam2peaks-nf -r latest -profile singularity --input_file input.tsv --ref hg38 --gencode gencode.bed --output_folder output --ignoreDuplicates

To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).

Chip-seq mode

To use the pipeline for Chip-seq, add the --chip flag :

nextflow run iarcbioinfo/bam2peaks-nf -r latest -profile singularity --input_file input.tsv --ref hg38 --gencode gencode.bed --output_folder output --mode chip --broad --extsize 320

Output

Type	Description
bw/	Outputs of bamCoverage in bigWig format
Counts/	With --saturation return the number of reads for each subsets
Peaks	Peaks computed by MACS
Peaks_intersect	Peaks intersections computed by idr
QCs	deeptools graphics
Saturation_peaks	With --saturation, all peaks files for each subsets

Contributions

Name	Email	Description
Vincent Cahais	CahaisV@iarc.who.int	Developer to contact for support
Claire Renard	Renardc@iarc.who.int	Developer