Workflow Type: Galaxy

This workflow takes as input a collection of fastqs (single reads). Remove adapters with cutadapt, map with bowtie2. Keep MAPQ30. MACS2 for bam with fixed extension or model.

Inputs

ID Name Description Type
SR fastq input #main/SR fastq input Should be a collection with ChIPseq fastqs
  • array containing
    • File
adapter_forward #main/adapter_forward Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
  • 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
5 Cutadapt (remove adapter + bad quality bases) toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0
6 Bowtie2 map on reference toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0
7 filter MAPQ30 toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1
8 Call Peaks with MACS2 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0
9 summary of MACS2 summary of MACS2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
10 Bigwig from MACS2 wig_to_bigWig
11 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1

Outputs

ID Name Description Type
MACS2 narrowPeak #main/MACS2 narrowPeak n/a
  • File
MACS2 peaks #main/MACS2 peaks n/a
  • File
MACS2 report #main/MACS2 report n/a
  • File
MACS2 summits #main/MACS2 summits 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
coverage from MACS2 #main/coverage from MACS2 n/a
  • File
filtered BAM #main/filtered BAM n/a
  • File
mapping stats #main/mapping stats n/a
  • File

Version History

v0.9 (latest) Created 30th Apr 2024 at 03:02 by WorkflowHub Bot

Updated to v0.9


Frozen v0.9 924fbb6

v0.5 Created 18th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.5


Frozen v0.5 56e6f3b

v0.4 Created 1st Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.4


Frozen v0.4 1a21f69

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

Updated to v0.3


Frozen v0.3 906ba40

v0.2 Created 29th Nov 2022 at 03:01 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 97c1b8e

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

Updated to v0.1


Frozen v0.1 8963174
help Creators and Submitter
Creator
  • Lucille Delisle
Additional credit

Lucille Delisle

Submitter
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Views: 2787

Created: 21st Oct 2022 at 03:01

Last updated: 1st Sep 2023 at 03:01

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