atacseq

Summary

This pipeline calls signals of single-cell ATAC-seq data using MACS2.

The following steps are performed (modelled after Buenrostro et al., (2015)):

The input reads (assumed to be adapter trimmed) are mapped with Bowtie2 and iscordant and unaligned reads are immediately dropped
Duplicates are then marked with Sambamba
Duplicated reads as well as those with low mapping quality (Q30) and reads not mapping against autosomes (see cfg/references.yaml) are removed
Peaks are called with MACS2 (broad and narrow). Peaks summits are converted to bed files (extended with --peak-ext-bp)-
MACS2 is run with --nomodel -f BAMPE --nolambda --call-summits for PE data and --nomodel --shift -100 --extsize 200 for SE data (see --shift and --extsize for SE specific MACS2 options)

Input

The input reads are assumed to be adapter trimmed
Fragment length for Bowtie can be set with --fragment-length
For default references see option --references-cfg and cfg/references.yaml

Output

Results appear per sample in out/{sample}/
Filtered BAM file: out/{sample}/{sample}.bowtie2.dedup.flt.bam
Mapping stats are named as bamfiles with stats attached
Called peaks and their coordinates out/{sample/macs2-{peaktype}/{sample}_peaks.xls
Extended peak summit location out/{sample}/macs2-{peaktype}/{sample}_summits.bed
Tag density profile out/{sample}/macs2-{peaktype}/{sample}_treat_pileup.bw

where {peaktype} is 'narrow' or 'broad'

References