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Run on GalaxyComplete ChIP-seq analysis for paired-end sequencing data. Processes raw FASTQ files through adapter removal (fastp), alignment to reference genome (Bowtie2), and stringent quality filtering (MAPQ greater than 30, concordant pairs only). Peak calling with MACS2 optimized for paired-end reads identifies protein-DNA binding sites. Generates alignment files, coverage, peak calls, and quality metrics for downstream analysis.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| 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 |
|
| PE fastq input | #main/PE fastq input | Should be a paired collection with ChIPseq fastqs |
|
| Percentage of bad quality bases per read | #main/Percentage of bad quality bases per read | fastp will discard any read which has more than this percentage of bases with a quality below 30, use 100 to not filter reads based on quality. We recommend to use a value that corresponds approximately to 15bp of good quality (for 100bp reads use 85, for 50bp use 70) |
|
| Reference genome | #main/Reference genome | Choose a reference genome to map on |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | Fastp (remove adapter and bad quality reads) | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy2 |
| 6 | Bowtie2 map on reference | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0 |
| 7 | filter MAPQ30 concordent pairs | 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/9.5+galaxy2 |
| 10 | Bigwig from MACS2 | wig_to_bigWig |
| 11 | 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
v0.1 (earliest) Created 21st Oct 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1e8fa694
Creators and Submitter
Views: 15465 Downloads: 17158 Runs: 1
Created: 21st Oct 2022 at 03:01
Last updated: 20th Aug 2025 at 10:16
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