cutandrun/main
Version 1

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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.

SEEK ID: https://workflowhub.eu/workflows/846?version=1

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/4.8+galaxy0
7 Bowtie2 map on reference toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0
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/2.30.0+galaxy2
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/1.11+galaxy1

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

v0.10 (earliest) Created 1st May 2024 at 03:02 by WorkflowHub Bot

Updated to v0.10


Frozen v0.10 8e12b20
help Creators and Submitter
Creator
  • Lucille Delisle
Submitter
Tools
Cutadapt
Bowtie 2
SAMtools
BEDTools
MACS
MultiQC
License
MIT License
Activity

Views: 118

Created: 1st May 2024 at 03:02

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Total size: 20.6 MB
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