ATAC-seq GTM

epigenetics-atac-seq/main-workflow

Author(s)

Version
10
Last updated
May 10, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
epigenetics

Features
Tutorial
ATAC-Seq data analysis
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00063
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
output
out_file1
output
out2
out1
out2
out1
output
out_file1
outFile
outFile
output
output_treat_pileup
out_file1
output
out_file1
output_narrowpeaks
output
output
out_file1
output
outFileName
outFileName
ℹ️ Input Dataset
bed file with genes
ℹ️ Input Dataset
ctcf peaks
ℹ️ Input Dataset
ATAC R2 read in fastq.gz format
ℹ️ Input Dataset
ATAC R1 read in fastq.gz format
Filter
FastQC
ATAC remove nextera adapters with cutadapt
FastQC
bedtools Intersect intervals
FastQC
Bowtie2
FastQC
Filter BAM ATAC
MarkDuplicates
bedtools BAM to BED
Paired-end histogram
MACS2 callpeak
Wig/BedGraph-to-bigWig
computeMatrix
pyGenomeTracks
computeMatrix
plotHeatmap
plotHeatmap
Output
computeMatrix on input dataset(s): Matrix
Output
plotHeatmap on input dataset(s): Image

Inputs

Input Label
Input dataset bed file with genes
Input dataset ctcf peaks
Input dataset ATAC R2 read in fastq(.gz) format
Input dataset ATAC R1 read in fastq(.gz) format

Outputs

From Output Label
Filter1 Filter
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 Cutadapt ATAC remove nextera adapters with cutadapt
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0 bedtools Intersect intervals
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0 Bowtie2
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 Filter Filter BAM ATAC
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 MarkDuplicates
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0 bedtools BAM to BED
toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1 Paired-end histogram
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6 MACS2 callpeak
wig_to_bigWig Wig/BedGraph-to-bigWig
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 computeMatrix
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6 pyGenomeTracks
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 computeMatrix
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1 plotHeatmap
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1 plotHeatmap

Tools

Tool Links
Filter1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 View in ToolShed
wig_to_bigWig

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
20 96d212779 2021-04-29 16:26:19 update deeptools tools + parameters
19 ba3bf335e 2021-04-12 14:41:50 use pygenometracks 3.6
18 af99da9c0 2021-04-02 16:42:29 update the workflow
17 d5cd0ab56 2021-03-30 15:33:26 update tutorial
16 d4aee8b0d 2020-06-16 09:02:06 change bedtools to allow to sort encodePeak
15 c1cf1143c 2020-06-11 07:22:17 macs2 to MACS2 in figures and workflow
14 69d703ece 2020-06-11 06:10:41 add tag and annotation
13 83f254a2b 2020-06-10 21:28:18 update new version of pgt
12 667ff3de9 2020-01-22 10:59:29 annotation
11 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
10 05fb8eedb 2019-12-20 09:55:47 New workflows unflattened
9 2ebad4e59 2019-12-20 09:53:24 rebase
8 bc9c7ce8a 2019-12-19 15:51:45 changed awk step
7 1bef60c2d 2019-12-19 15:17:31 updated workflow
6 faf6d298a 2019-12-12 13:02:33 unflatten workflows
5 397de5ef9 2019-08-27 13:33:45 modified version of genrich and pygenometracks
4 93027360b 2019-08-15 08:08:49 Changes to workflow atac
3 b2bcfc0d7 2019-07-06 12:40:48 Add visualisation step to workflow (pygenometracks)
2 7dec9b919 2019-07-05 14:15:22 Updates to workflow
1 bb008c8c9 2019-07-05 13:24:04 First draft of ATAC-seq tut from CoFest (WIP)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows