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Tests Complete CUT&RUN/CUT&TAG analysis workflow for paired-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt) and alignment (Bowtie2 with dovetail option enabled). Applies quality filtering (MAPQ ≥ 30, concordant pairs only), converts BAM to BED format, and performs peak calling using MACS2 with parameters optimized for the punctate signal profile characteristic of CUT&RUN/CUT&TAG experiments.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| PE fastq input | #main/PE fastq input | Should be a paired collection with CUT and RUN fastqs |
|
| adapter_forward | #main/adapter_forward | Please use: For R1: - For TrueSeq (CUT and RUN): GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTCCGAGCCCACGAGAC |
|
| adapter_reverse | #main/adapter_reverse | Please use: For R2: - For TruSeq (CUT and RUN): GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTGACGCTGCCGACGA |
|
| 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 Reads |
|
| 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/5.2+galaxy1 |
| 7 | Bowtie2 map on reference | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.5+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/2.31.1+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/9.5+galaxy3 |
| 13 | Bigwig from MACS2 | wig_to_bigWig |
| 14 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| BAM filtered rmDup | #main/BAM filtered rmDup | n/a |
|
| Coverage from MACS2 (bigwig) | #main/Coverage from MACS2 (bigwig) | n/a |
|
| MACS2 narrowPeak | #main/MACS2 narrowPeak | n/a |
|
| MACS2 peaks xls | #main/MACS2 peaks xls | n/a |
|
| MACS2 report | #main/MACS2 report | n/a |
|
| MACS2 summits | #main/MACS2 summits | n/a |
|
| Mapping stats | #main/Mapping stats | n/a |
|
| MarkDuplicates metrics | #main/MarkDuplicates metrics | n/a |
|
| MultiQC on input dataset(s): Stats | #main/MultiQC on input dataset(s): Stats | n/a |
|
| MultiQC webpage | #main/MultiQC webpage | n/a |
|
Version History
v0.18 (latest) Created 8th Apr 2026 at 03:01 by WorkflowHub Bot
Updated to v0.18
Frozen
v0.18e214a55
v0.1 (earliest) Created 20th Oct 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
308e6ab
Creators and Submitter
Views: 17412 Downloads: 38223 Runs: 5
Created: 20th Oct 2022 at 03:01
Last updated: 21st Jan 2023 at 03:01
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