Workflow Type: Galaxy

This workflow take as input a collection of paired fastq. Remove adapters with cutadapt, map pairs with bowtie2 allowing dovetail. Keep MAPQ30 and concordant pairs. BAM to BED. MACS2 with "ATAC" parameters.

Inputs

ID Name Description Type
PE fastq input #main/PE fastq input Should be a paired collection with CUT and RUN fastqs
  • array containing
    • File
adapter_forward #main/adapter_forward Please use: For R1: - For TrueSeq (CUT and RUN): GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
  • string
adapter_reverse #main/adapter_reverse Please use: For R2: - For TruSeq (CUT and RUN): GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTGACGCTGCCGACGA
  • string
effective_genome_size #main/effective_genome_size Used by MACS2: H. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000
  • int
normalize_profile #main/normalize_profile Whether you want to have a profile normalized as Signal to Million Reads
  • boolean
reference_genome #main/reference_genome reference_genome
  • string

Steps

ID Name Description
6 Cutadapt (remove adapter + bad quality bases) toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
7 Bowtie2 map on reference toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1
8 filter MAPQ30 concordant pairs toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1
9 remove PCR duplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
10 convert BAM to BED to improve peak calling toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0
11 Call Peaks with MACS2 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0
12 summary of MACS2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
13 Bigwig from MACS2 wig_to_bigWig
14 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0

Outputs

ID Name Description Type
BAM filtered rmDup #main/BAM filtered rmDup n/a
  • File
Coverage from MACS2 (bigwig) #main/Coverage from MACS2 (bigwig) n/a
  • File
MACS2 narrowPeak #main/MACS2 narrowPeak n/a
  • File
MACS2 peaks xls #main/MACS2 peaks xls n/a
  • File
MACS2 report #main/MACS2 report n/a
  • File
MACS2 summits #main/MACS2 summits n/a
  • File
Mapping stats #main/Mapping stats n/a
  • File
MarkDuplicates metrics #main/MarkDuplicates metrics n/a
  • File
MultiQC on input dataset(s): Stats #main/MultiQC on input dataset(s): Stats n/a
  • File
MultiQC webpage #main/MultiQC webpage n/a
  • File

Version History

v0.13 (latest) Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

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v0.6.1 Created 24th Nov 2023 at 03:03 by WorkflowHub Bot

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v0.6 Created 20th Oct 2023 at 03:02 by WorkflowHub Bot

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v0.1 (earliest) Created 20th Oct 2022 at 03:01 by WorkflowHub Bot

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help Creators and Submitter
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  • Lucille Delisle
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Created: 20th Oct 2022 at 03:01

Last updated: 21st Jan 2023 at 03:01

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