Hi-C Analysis with Galaxy Tutorial Workflow 1.0
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Run on GalaxyWorkflow for the GTN tutorial: "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer".
Associated Tutorial
This workflows is part of the tutorial Hi-C analysis of Drosophila melanogaster cells using HiCExplorer, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Tristan Reynolds
Tutorial Author(s): Joachim Wolff, Fidel Ramirez, Vivek Bhardwaj, Ekaterina Polkh
Tutorial Contributor(s): Tristan Reynolds, Helena Rasche, Saskia Hiltemann, Nicola Soranzo, Joachim Wolff, Björn Grüning, Mehmet Tekman, Anup Kumar, Torsten Houwaart, Bérénice Batut, Niall Beard
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg, Collaborative Research Centre 992, The University of Melbourne, Melbourne Bioinformatics, Australian BioCommons
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GM12878_25kb_cooler_coarsen.cool | GM12878_25kb_cooler_coarsen.cool | n/a |
|
| H3K27me3.bw | H3K27me3.bw | n/a |
|
| H3K36me3.bw | H3K36me3.bw | n/a |
|
| H4K16ac.bw | H4K16ac.bw | n/a |
|
| HiC_S2_1p_10min_lowU_R1.fastq.gz | HiC_S2_1p_10min_lowU_R1.fastq.gz | n/a |
|
| HiC_S2_1p_10min_lowU_R2.fastq.gz | HiC_S2_1p_10min_lowU_R2.fastq.gz | n/a |
|
| corrected_contact_matrix_dm3_large.h5 | corrected_contact_matrix_dm3_large.h5 | n/a |
|
| dm3_genes.bed | dm3_genes.bed | n/a |
|
| dm3_genome.fasta | dm3_genome.fasta | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 9 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 |
| 10 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1 |
| 11 | hicFindRestSite | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindrestrictionsites/hicexplorer_hicfindrestrictionsites/3.7.6+galaxy1 |
| 12 | hicInfo | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicinfo/hicexplorer_hicinfo/3.7.6+galaxy1 |
| 13 | hicDetectLoops | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicdetectloops/hicexplorer_hicdetectloops/3.7.6+galaxy1 |
| 14 | hicInfo | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicinfo/hicexplorer_hicinfo/3.7.6+galaxy1 |
| 15 | hicPCA | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/3.6+galaxy1 |
| 16 | hicFindTADs | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/3.7.6+galaxy1 |
| 17 | hicBuildMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/3.7.6+galaxy1 |
| 18 | hicPlotMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1 |
| 19 | hicPlotMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1 |
| 20 | hicPlotMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1 |
| 21 | pyGenomeTracks | toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2 |
| 22 | hicCorrectMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.7.6+galaxy1 |
| 23 | hicMergeMatrixBins | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/3.7.6+galaxy1 |
| 24 | hicCorrectMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.7.6+galaxy1 |
| 25 | hicPlotMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1 |
| 26 | hicPlotMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1 |
Version History
master
Creators and Submitter
Views: 33 Downloads: 3 Runs: 0
Created: 11th Aug 2025 at 14:14
Tags AttributionsNone
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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!
