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Run on GalaxyComplete ChIP-seq analysis for paired-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and stringent quality filtering (MAPQ >= 30, concordant pairs only). Peak calling with MACS2 optimized for paired-end reads identifies protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| PE fastq input | #main/PE fastq input | Should be a paired collection with ChIPseq fastqs |
|
| adapter_forward | #main/adapter_forward | Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC |
|
| adapter_reverse | #main/adapter_reverse | Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT |
|
| effective_genome_size | #main/effective_genome_size | Used by MACS2: H. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000 |
|
| normalize_profile | #main/normalize_profile | Whether you want to have a profile normalized as Signal to Million Fragments |
|
| reference_genome | #main/reference_genome | reference_genome |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | Cutadapt (remove adapter + bad quality bases) | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0 |
| 7 | Bowtie2 map on reference | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 |
| 8 | filter MAPQ30 concordent pairs | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
| 9 | Call Peaks with MACS2 | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0 |
| 10 | summary of MACS2 | summary of MACS2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2 |
| 11 | Bigwig from MACS2 | wig_to_bigWig |
| 12 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| MACS2 narrowPeak | #main/MACS2 narrowPeak | n/a |
|
| MACS2 peaks | #main/MACS2 peaks | n/a |
|
| MACS2 report | #main/MACS2 report | n/a |
|
| MACS2 summits | #main/MACS2 summits | n/a |
|
| MultiQC on input dataset(s): Stats | #main/MultiQC on input dataset(s): Stats | n/a |
|
| MultiQC webpage | #main/MultiQC webpage | n/a |
|
| coverage from MACS2 | #main/coverage from MACS2 | n/a |
|
| filtered BAM | #main/filtered BAM | n/a |
|
| mapping stats | #main/mapping stats | n/a |
|
Version History
v0.15 (latest) Created 31st Jul 2025 at 03:02 by WorkflowHub Bot
Updated to v0.15
Frozen
v0.15da62ff5
v0.1 (earliest) Created 21st Oct 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
e8fa694
Creators and Submitter
Views: 15133 Downloads: 16841 Runs: 1
Created: 21st Oct 2022 at 03:01
Last updated: 20th Aug 2025 at 10:16
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