GTN - ChIP Seq - Formation Of Super Structures On Xi

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Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial GTN - ChIP Seq - Formation Of Super Structures On Xi, available in the GTN

Features

Thanks to...

Tutorial Author(s): Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Pavankumar Videm

Workflow Author(s): Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Leily Rabbani, Pavankumar Videm

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1153?version=2

Inputs

ID Name Description Type
wt_CTCF_rep1.bam wt_CTCF_rep1.bam n/a
  • File
wt_CTCF_rep2.bam wt_CTCF_rep2.bam n/a
  • File
wt_H3K27me3_rep1.bam wt_H3K27me3_rep1.bam n/a
  • File
wt_H3K27me3_rep2.bam wt_H3K27me3_rep2.bam n/a
  • File
wt_H3K4me3_read1.fastq.gz wt_H3K4me3_read1.fastq.gz n/a
  • File
wt_H3K4me3_read2.fastq.gz wt_H3K4me3_read2.fastq.gz n/a
  • File
wt_H3K4me3_rep1.bam wt_H3K4me3_rep1.bam n/a
  • File
wt_H3K4me3_rep2.bam wt_H3K4me3_rep2.bam n/a
  • File
wt_input_rep1.bam wt_input_rep1.bam n/a
  • File
wt_input_rep2.bam wt_input_rep2.bam n/a
  • File

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
  • File
wt_H3K4me3_rep1_trim_galore wt_H3K4me3_rep1_trim_galore n/a
  • File
wt_H3K4me3_rep1_read1_fastqc wt_H3K4me3_rep1_read1_fastqc n/a
  • File
wt_H3K4me3_rep1_bamcoverage wt_H3K4me3_rep1_bamcoverage n/a
  • File
wt_H3K4me3_rep1_idxstats wt_H3K4me3_rep1_idxstats n/a
  • File
wt_H3K4me3_input_rep1_macs2 wt_H3K4me3_input_rep1_macs2 n/a
  • File
wt_H3K4me3_input_rep1_bamcompare wt_H3K4me3_input_rep1_bamcompare n/a
  • File
wt_H3K4me3_rep1_bowtie2 wt_H3K4me3_rep1_bowtie2 n/a
  • File
wt_H3K4me3_CTCF_rep1_mergebed wt_H3K4me3_CTCF_rep1_mergebed n/a
  • File
wt_all_mergebed wt_all_mergebed n/a
  • File

Version History

5.0 (latest) Created 16th Jul 2024 at 14:06 by Helena Rasche

Added/updated 4 files


Open master 5c9a6e6

7.0 (earliest) Created 25th Jun 2024 at 11:04 by Helena Rasche

Added/updated 4 files


Frozen 7.0 641a184
help Creators and Submitter
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Tools
FastQC
Trim Galore
SAMtools
DeepTools
MACS
Bowtie 2
BEDTools
License
Creative Commons Attribution 4.0 International
Activity

Views: 190   Downloads: 67

Created: 25th Jun 2024 at 11:04

Last updated: 25th Jun 2024 at 11:04

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