sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)

transcriptomics-srna/srna-seq-step-1-read-preprocessing-and-removal-of-artifacts

Author(s)

Version
2
Last updated
Jan 17, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics

Features
Tutorial
Differential abundance testing of small RNAs
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00255
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nInput dataset collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nrRNA reference FASTA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nmiRNA hairpin reference FASTA"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["FastQC"];
  0 -->|output| 3;
  4["Trim Galore!"];
  0 -->|output| 4;
  5["FastQC"];
  4 -->|trimmed_reads_single| 5;
  6["HISAT"];
  4 -->|trimmed_reads_single| 6;
  1 -->|output| 6;
  7["Filter SAM or BAM, output SAM or BAM"];
  6 -->|output_alignments| 7;
  8["Convert from BAM to FastQ"];
  7 -->|output1| 8;
  9["HISAT"];
  8 -->|output| 9;
  2 -->|output| 9;
  10["Filter SAM or BAM, output SAM or BAM"];
  9 -->|output_alignments| 10;
  11["Convert from BAM to FastQ"];
  10 -->|output1| 11;
  12["Manipulate FASTQ"];
  11 -->|output| 12;
  13["Manipulate FASTQ"];
  11 -->|output| 13;
  14["FastQC"];
  12 -->|output_file| 14;
  15["FastQC"];
  13 -->|output_file| 15;

Inputs

Input Label
Input dataset collection
Input dataset rRNA reference FASTA
Input dataset miRNA hairpin reference FASTA

Outputs

From Output Label
Input dataset collection
Input dataset rRNA reference FASTA
Input dataset miRNA hairpin reference FASTA
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2 Trim Galore!
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65 FastQC
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0 Convert from BAM to FastQ
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0 Convert from BAM to FastQ

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3 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 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
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 6efea8d06 2017-06-29 10:21:58 Move the srna tutorial to transcriptomics topic

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.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