CUT&RUN 3.0
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Run on GalaxyCUT&RUN workflow used in GTN
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 , Pavankumar Videm
Tutorial Author(s): Florian Heyl, Pavankumar Videm
Tutorial Contributor(s): Helena Rasche, Lucille Delisle, Wolfgang Maier, Florian Heyl, Saskia Hiltemann, Björn Grüning, Pavankumar Videm
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GATA1 ChIP-Seq peaks | GATA1 ChIP-Seq peaks | n/a |
|
| I certify that I am not using this workflow for commercial purposes | I certify that I am not using this workflow for commercial purposes | n/a |
|
| Input Dataset Collection | Input Dataset Collection | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Trim Galore! | toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy1 |
| 4 | Flatten collection | __FLATTEN__ |
| 5 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 |
| 6 | Falco | toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 |
| 7 | plotFingerprint | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0 |
| 8 | Filter BAM | toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2 |
| 9 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 10 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0 |
| 11 | Select | Grep1 |
| 12 | Falco | toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 |
| 13 | bedtools BAM to BED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0 |
| 14 | Paired-end histogram | toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.2 |
| 15 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1 |
| 16 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 17 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0 |
| 18 | Extract dataset | __EXTRACT_DATASET__ |
| 19 | Extract dataset | __EXTRACT_DATASET__ |
| 20 | Wig/BedGraph-to-bigWig | wig_to_bigWig |
| 21 | bedtools Intersect intervals | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 |
| 22 | bedtools Intersect intervals | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 |
| 23 | Extract Genomic DNA | toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy3 |
| 24 | computeMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0 |
| 25 | MEME-ChIP | toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1 |
| 26 | plotHeatmap | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| output | output | n/a |
|
| outFileName | outFileName | n/a |
|
Version History
master
Creators and Submitter
Views: 51 Downloads: 7 Runs: 0
Created: 2nd Jun 2025 at 10:58
Tags AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
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Teams: Galaxy Training Network
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The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
