RNA Seq Reads To Counts

transcriptomics-rna-seq-reads-to-counts/rna-seq-reads-to-counts

Author(s)

version Version
4
last_modification Last updated
Jan 23, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
transcriptomics

Features

Tutorial
hands_on 1: RNA-Seq reads to counts
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00251
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Collection\nInput FASTQs collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput Reference gene BED"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Infer Experiment"];
  5 -->|output_alignments| 10;
  1 -->|output| 10;
  11["Read Distribution"];
  5 -->|output_alignments| 11;
  1 -->|output| 11;
  12["Column Join"];
  6 -->|output_short| 12;
  13["MultiQC"];
  4 -->|text_file| 13;
  3 -->|report| 13;
  10 -->|output| 13;
  7 -->|metrics_file| 13;
  8 -->|output| 13;
  9 -->|outputtxt| 13;
  11 -->|output| 13;
  6 -->|output_summary| 13;
  5 -->|summary_file| 13;
  2["FastQC raw reads"];
  0 -->|output| 2;
  3["Cutadapt"];
  0 -->|output| 3;
  4["FastQC post QC"];
  3 -->|out1| 4;
  5["HISAT2"];
  3 -->|out1| 5;
  6["featureCounts"];
  5 -->|output_alignments| 6;
  7["MarkDuplicates"];
  5 -->|output_alignments| 7;
  8["Samtools idxstats"];
  5 -->|output_alignments| 8;
  9["Gene Body Coverage BAM"];
  5 -->|output_alignments| 9;
  1 -->|output| 9;

Inputs

Input Label
Input dataset collection Input FASTQs collection
Input dataset Input Reference gene BED

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1 View in ToolShed

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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • 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”
  • 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
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 361236c41 2019-04-04 09:00:14 Changed format of workflows
1 0ea8c7901 2018-12-30 07:40:49 Rename tutorial and image folders to the updated titles

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.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