Workflow Type: Galaxy

This workflow take as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will plot the number of reads for each fragment length.


ID Name Description Type
PE fastq input PE fastq input Should be a paired collection with ATAC-seq fastqs
  • File[]
effective_genome_size effective_genome_size Used by macs2:\nH. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000
  • int
reference_genome reference_genome reference_genome
  • string


ID Name Description
3 Cutadapt (remove adapter + bad quality bases)
4 Bowtie2 map on reference
5 filter MAPQ30 concordant pairs and not mitochondrial pairs
6 Get number of reads per chromosome
7 remove PCR duplicates
8 reads in chrM/MT for multiQC
9 convert BAM to BED to improve peak calling
10 Compute fragment length histogram
11 number of reads
12 Call Peak with MACS2
13 get summits +/-500kb
14 summary of MACS2
15 Bigwig from MACS2 wig_to_bigWig
16 Merge summits +/-500kb
17 Compute coverage on summits +/-500kb
18 number of reads in peaks
19 Combine number of reads in peaks with total number of reads cat1
20 reads in peaks multiQC
21 MultiQC


ID Name Description Type
mapping stats mapping stats n/a
  • File
MarkDuplicates metrics MarkDuplicates metrics n/a
  • File
BAM filtered rmDup BAM filtered rmDup n/a
  • File
histogram of fragment length histogram of fragment length n/a
  • File
MACS2 narrowPeak MACS2 narrowPeak n/a
  • File
MACS2 report MACS2 report n/a
  • File
Coverage from MACS2 (bigwig) Coverage from MACS2 (bigwig) n/a
  • File
1kb around summits 1kb around summits n/a
  • File
Nb of reads in summits +-500bp Nb of reads in summits +-500bp n/a
  • File
MultiQC on input dataset(s): Stats MultiQC on input dataset(s): Stats n/a
  • File
MultiQC webpage MultiQC webpage n/a
  • File

Version History

v0.4 (latest) Created 17th Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.4

Frozen v0.4 a465610

v0.3 Created 14th Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.3

Frozen v0.3 5f2a283

v0.2 Created 30th Nov 2022 at 03:01 by WorkflowHub Bot

Updated to v0.2

Frozen v0.2 e36373a

v0.1 (earliest) Created 21st Oct 2022 at 03:01 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 1071145
help Creators and Submitter
  • Lucille Delisle
Additional credit

Lucille Delisle


Views: 195

Created: 21st Oct 2022 at 03:01

Last updated: 17th Jan 2023 at 03:01

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