GTN - ChIP Seq - Formation Of Super Structures On Xi 5.0
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This workflows is part of the tutorial Formation of the Super-Structures on the Inactive X, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Pavankumar Videm
Tutorial Author(s): Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Pavankumar Videm
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| wt_CTCF_rep1.bam | wt_CTCF_rep1.bam | n/a |
|
| wt_CTCF_rep2.bam | wt_CTCF_rep2.bam | n/a |
|
| wt_H3K27me3_rep1.bam | wt_H3K27me3_rep1.bam | n/a |
|
| wt_H3K27me3_rep2.bam | wt_H3K27me3_rep2.bam | n/a |
|
| wt_H3K4me3_read1.fastq.gz | wt_H3K4me3_read1.fastq.gz | n/a |
|
| wt_H3K4me3_read2.fastq.gz | wt_H3K4me3_read2.fastq.gz | n/a |
|
| wt_H3K4me3_rep1.bam | wt_H3K4me3_rep1.bam | n/a |
|
| wt_H3K4me3_rep2.bam | wt_H3K4me3_rep2.bam | n/a |
|
| wt_input_rep1.bam | wt_input_rep1.bam | n/a |
|
| wt_input_rep2.bam | wt_input_rep2.bam | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 11 | Trim Galore! | toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0 |
| 12 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 13 | Samtools idxstats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4 |
| 14 | bamCoverage | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0 |
| 15 | bamCoverage | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0 |
| 16 | bamCoverage | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0 |
| 17 | Samtools idxstats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4 |
| 18 | plotFingerprint | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0 |
| 19 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 20 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0 |
| 21 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 22 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 23 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0 |
| 24 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 25 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 26 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0 |
| 27 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 28 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0 |
| 29 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 30 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0 |
| 31 | multiBamSummary | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.1.0.0 |
| 32 | bamCompare | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0 |
| 33 | MACS2 callpeak | toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0 |
| 34 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0 |
| 35 | Concatenate datasets | cat1 |
| 36 | plotCorrelation | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0 |
| 37 | Concatenate datasets | cat1 |
| 38 | bedtools SortBED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2 |
| 39 | bedtools SortBED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2 |
| 40 | bedtools MergeBED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0 |
| 41 | bedtools MergeBED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0 |
| 42 | computeMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.1.0.0 |
| 43 | computeMatrix | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.1.0.0 |
| 44 | plotHeatmap | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.1.0.1 |
| 45 | plotHeatmap | toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.1.0.1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| wt_H3K4me3_rep1_read2_fastqc | wt_H3K4me3_rep1_read2_fastqc | n/a |
|
| wt_H3K4me3_rep1_trim_galore | wt_H3K4me3_rep1_trim_galore | n/a |
|
| wt_H3K4me3_rep1_read1_fastqc | wt_H3K4me3_rep1_read1_fastqc | n/a |
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| wt_H3K4me3_rep1_bamcoverage | wt_H3K4me3_rep1_bamcoverage | n/a |
|
| wt_H3K4me3_rep1_idxstats | wt_H3K4me3_rep1_idxstats | n/a |
|
| wt_H3K4me3_input_rep1_macs2 | wt_H3K4me3_input_rep1_macs2 | n/a |
|
| wt_H3K4me3_input_rep1_bamcompare | wt_H3K4me3_input_rep1_bamcompare | n/a |
|
| wt_H3K4me3_rep1_bowtie2 | wt_H3K4me3_rep1_bowtie2 | n/a |
|
| wt_H3K4me3_CTCF_rep1_mergebed | wt_H3K4me3_CTCF_rep1_mergebed | n/a |
|
| wt_all_mergebed | wt_all_mergebed | n/a |
|
Version History
master
Creators and Submitter
Views: 1146 Downloads: 163 Runs: 0
Created: 2nd Jun 2025 at 11:01
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