Workflow Type: Galaxy

CUT&RUN workflow used in GTN

Associated Tutorial

This workflows is part of the tutorial CUT&RUN data analysis, available in the GTN

Features

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

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
GATA1 ChIP-Seq peaks GATA1 ChIP-Seq peaks n/a
  • File
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
  • boolean
Input Dataset Collection Input Dataset Collection n/a
  • File[]

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
  • File
outFileName outFileName n/a
  • File

Version History

3.0 (earliest) Created 2nd Jun 2025 at 10:58 by GTN Bot

Added/updated 4 files


Open master 15b57b6
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Created: 2nd Jun 2025 at 10:58

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