atacseq/main
Version 1

Workflow Type: Galaxy
Tests: Passing

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.

Inputs

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

Steps

ID Name Description
3 Cutadapt (remove adapter + bad quality bases) toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0
4 Bowtie2 map on reference toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1
5 filter MAPQ30 concordant pairs and not mitochondrial pairs toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.1+galaxy0
6 Get number of reads per chromosome toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4
7 remove PCR duplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3
8 reads in chrM/MT for multiQC toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
9 convert BAM to BED to improve peak calling toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2
10 Compute fragment length histogram toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1
11 number of reads toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
12 Call Peak with MACS2 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0
13 get summits +/-500kb toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1
14 summary of MACS2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
15 Bigwig from MACS2 wig_to_bigWig
16 Merge summits +/-500kb toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0
17 Compute coverage on summits +/-500kb toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0
18 number of reads in peaks toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
19 Combine number of reads in peaks with total number of reads cat1
20 reads in peaks multiQC toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
21 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0

Outputs

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

Version 1 (earliest) Created 23rd Nov 2022 at 10:41 by Finn Bacall

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Frozen Version-1 938dbc5
help Creators and Submitter
Creator
  • Lucille Delisle
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Views: 28

Created: 23rd Nov 2022 at 10:41

Last used: 28th Nov 2022 at 20:42

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