Workflow Type: Galaxy
Frozen
Frozen
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 |
|
adapter_forward | #main/adapter_forward | Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC |
|
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 |
---|---|---|
5 | Cutadapt (remove adapter + bad quality bases) | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1 |
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+galaxy0 |
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 |
|
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
v0.12 (latest) Created 7th Oct 2024 at 16:33 by WorkflowHub Bot
Updated to v0.12
Frozen
v0.12
7605642
v0.1 (earliest) Created 21st Oct 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
8963174