This workflow does not specify a "main" workflow file.
Workflow Type: Galaxy
CUT&RUN (and CUT&TAG) Workflow
Inputs dataset
- The workflow needs a single input which is a list of dataset pairs of fastqsanger.
Inputs values
- adapter sequences: this depends on the library preparation. Usually CUT&RUN is Truseq and CUT&TAG is Nextera. If you don't know, use FastQC to determine if it is Truseq or Nextera
- reference_genome: this field will be adapted to the genomes available for bowtie2
- effective_genome_size: this is used by macs2 and may be entered manually (indications are provided for heavily used genomes)
Processing
- The workflow will remove illumina adapters and low quality bases and filter out any read smaller than 15bp
- The filtered reads are mapped with bowtie2 allowing dovetail and fragment length up to 1kb
- The BAM is filtered to keep only MAPQ30 and concordant pairs
- The PCR duplicates are removed with Picard
- The BAM is converted to BED to enable macs2 to take both pairs into account
- The peaks are called with macs2 which at the same time generates a coverage file.
- The coverage file is converted to bigwig
- A multiQC is run to have an overview of the QC
Warning
- The coverage output is not normalized.
Inputs
ID | Name | Description | Type |
---|---|---|---|
PE fastq input | PE fastq input | Should be a paired collection with CUT and RUN fastqs |
|
adapter_forward | adapter_forward | Please use: For R1: - For TrueSeq (CUT and RUN): GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTCCGAGCCCACGAGAC |
|
adapter_reverse | adapter_reverse | Please use: For R2: - For TruSeq (CUT and RUN): GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTGACGCTGCCGACGA |
|
effective_genome_size | effective_genome_size | Used by MACS2: H. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000 |
|
reference_genome | reference_genome | reference_genome |
|
Steps
ID | Name | Description |
---|---|---|
5 | Cutadapt (remove adapter + bad quality bases) | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0 |
6 | Bowtie2 map on reference | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1 |
7 | filter MAPQ30 concordant pairs | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
8 | remove PCR duplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3 |
9 | convert BAM to BED to improve peak calling | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2 |
10 | Call Peaks with MACS2 | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0 |
11 | summary of MACS2 | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
12 | Bigwig from MACS2 | wig_to_bigWig |
13 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Mapping stats | Mapping stats | n/a |
|
MarkDuplicates metrics | MarkDuplicates metrics | n/a |
|
BAM filtered rmDup | BAM filtered rmDup | n/a |
|
MACS2 peaks xls | MACS2 peaks xls | n/a |
|
MACS2 summits | MACS2 summits | n/a |
|
MACS2 narrowPeak | MACS2 narrowPeak | n/a |
|
MACS2 report | MACS2 report | n/a |
|
Coverage from MACS2 (bigwig) | Coverage from MACS2 (bigwig) | n/a |
|
MultiQC webpage | MultiQC webpage | n/a |
|
MultiQC on input dataset(s): Stats | MultiQC on input dataset(s): Stats | n/a |
|
Version History
v0.13 (latest) Created 7th Oct 2024 at 16:33 by WorkflowHub Bot
Updated to v0.13
Frozen
v0.13
5352f5e
v0.1 (earliest) Created 20th Oct 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
308e6ab