Galaxy Workflow Galaxy Hi C 4.0
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Run on GalaxyHi-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
Thanks to...
Tutorial Author(s): Joachim Wolff, Fidel Ramirez, Vivek Bhardwaj, Ekaterina Polkh
Tutorial Contributor(s): 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
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| H3K27me3.bw | H3K27me3.bw | n/a |
|
| H3K36me3.bw | H3K36me3.bw | n/a |
|
| H4K16ac.bw | H4K16ac.bw | n/a |
|
| R1.fastq | R1.fastq | n/a |
|
| R2.fastq | R2.fastq | n/a |
|
| dm3_genes.bed | dm3_genes.bed | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0 |
| 7 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0 |
| 8 | hicBuildMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.0 |
| 9 | hicMergeMatrixBins | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.0 |
| 10 | hicCorrectMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.0 |
| 11 | hicCorrectMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.0 |
| 12 | hicPlotMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.0 |
| 13 | hicPlotMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.0 |
| 14 | hicFindTADs | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.0 |
| 15 | hicPCA | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.0 |
| 16 | hicPlotTADs | toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.0 |
Version History
master
Creators and Submitter
Views: 1152 Downloads: 166 Runs: 0
Created: 2nd Jun 2025 at 11:01
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