CUT&RUN GTN
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Download RO-CrateCUT&RUN data analysis workflow. It uses fastQC, trim adapters with Trim Galore!, map with Bowtie2, filter the BAM and mark duplicates. Peaks are called with MACS2 and peaks from both replicates are intersected and then intersected to the ChIP peaks. Finally MEME ChIP is run to get the motifs.
Associated Tutorial
This workflows is part of the tutorial CUT&RUN data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Florian Heyl
Tutorial Author(s): Florian Heyl
Tutorial Contributor(s): Helena Rasche, Lucille Delisle, Florian Heyl, Saskia Hiltemann, Björn Grüning
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Fastq PE inputs | Fastq PE inputs | Fastq PE inputs |
|
| GATA1_ChIP-Seq peaks | GATA1_ChIP-Seq peaks | n/a |
|
| Non-Commercial purposes | Non-Commercial purposes | I certify that I am not using this tool for commercial purposes. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Flatten collection for FastQC | __FLATTEN__ |
| 4 | Trim Galore! | toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0 |
| 5 | FastQC on raw reads | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 6 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 |
| 7 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0 |
| 8 | Filter BAM | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2 |
| 9 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0 |
| 10 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 11 | Paired-end histogram | toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1 |
| 12 | bedtools BAM to BED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0 |
| 13 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0 |
| 14 | Get Rep1 peaks | __EXTRACT_DATASET__ |
| 15 | Get Rep2 peaks | __EXTRACT_DATASET__ |
| 16 | Get Robust GATA1 CUT and RUN peaks | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 |
| 17 | Get True GATA1 CUT and RUN peaks | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 |
| 18 | Extract Genomic DNA | toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2 |
| 19 | Get motif | toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| MEME-ChIP html output | MEME-ChIP html output | n/a |
|
Version History
2.0 (latest) Created 24th Feb 2025 at 13:07 by Helena Rasche
Added/updated 4 files
Open
master2b4fdf5
1.0 (earliest) Created 25th Jun 2024 at 11:04 by Helena Rasche
Added/updated 4 files
Frozen
1.03332adf
Creators and Submitter
Views: 601 Downloads: 141
Created: 25th Jun 2024 at 11:04
Last updated: 24th Feb 2025 at 13:07
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