Genome-wide alternative splicing analysis: human
transcriptomics-differential-isoform-expression/main-workflow
Launch in Tutorial Mode
question
galaxy-download Download
galaxy-download Download
flowchart TD 0["ℹ️ Input Collection\nRNA-seq data collection"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nReference genome"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nGenome annotation"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nControl IDs"]; style 3 stroke:#2c3143,stroke-width:4px; 4["ℹ️ Input Parameter\nFactor 02"]; style 4 fill:#ded,stroke:#393,stroke-width:4px; 5["ℹ️ Input Parameter\nFactor 01"]; style 5 fill:#ded,stroke:#393,stroke-width:4px; 6["ℹ️ Input Dataset\nCPAT header"]; style 6 stroke:#2c3143,stroke-width:4px; 7["ℹ️ Input Dataset\nActive sites dataset"]; style 7 stroke:#2c3143,stroke-width:4px; 8["ℹ️ Input Dataset\nPfam-A HMM Stockholm file"]; style 8 stroke:#2c3143,stroke-width:4px; 9["ℹ️ Input Dataset\nPfam-A HMM library"]; style 9 stroke:#2c3143,stroke-width:4px; 10["fastp"]; 0 -->|output| 10; 11["Flatten collection"]; 0 -->|output| 11; 12["Search in textfiles"]; 2 -->|output| 12; 13["Search in textfiles"]; 2 -->|output| 13; 14["Convert GTF to BED12"]; 2 -->|output| 14; 15["FastQC"]; 11 -->|output| 15; 16["gffread"]; 12 -->|output| 16; 1 -->|output| 16; e34fd125-e860-48a2-9e58-bed5c3600b8d["Output\nlncRNA sequences"]; 16 --> e34fd125-e860-48a2-9e58-bed5c3600b8d; style e34fd125-e860-48a2-9e58-bed5c3600b8d stroke:#2c3143,stroke-width:4px; 17["gffread"]; 13 -->|output| 17; 1 -->|output| 17; 836eeb38-dc67-42df-93fa-2fcd5bbe7a80["Output\nprotein coding sequences"]; 17 --> 836eeb38-dc67-42df-93fa-2fcd5bbe7a80; style 836eeb38-dc67-42df-93fa-2fcd5bbe7a80 stroke:#2c3143,stroke-width:4px; 18["MultiQC"]; 15 -->|text_file| 18; 10 -->|report_json| 18; 19["Search in textfiles"]; 15 -->|text_file| 19; 20["Concatenate datasets"]; 19 -->|output| 20; 21["Search in textfiles"]; 20 -->|out_file1| 21; 22["Cut"]; 21 -->|output| 22; 23["Text reformatting"]; 22 -->|out_file1| 23; 24["Parse parameter value"]; 23 -->|outfile| 24; 25["RNA STAR"]; 2 -->|output| 25; 24 -->|integer_param| 25; 1 -->|output| 25; 10 -->|output_paired_coll| 25; 26["Concatenate datasets"]; 25 -->|splice_junctions| 26; 27["Text reformatting"]; 26 -->|out_file1| 27; 28["Cut"]; 27 -->|outfile| 28; 29["Sort"]; 28 -->|out_file1| 29; 30["Unique"]; 29 -->|out_file1| 30; 31["RNA STAR"]; 2 -->|output| 31; 24 -->|integer_param| 31; 1 -->|output| 31; 10 -->|output_paired_coll| 31; 30 -->|outfile| 31; 32["StringTie"]; 2 -->|output| 32; 31 -->|mapped_reads| 32; 33["Junction Annotation"]; 31 -->|mapped_reads| 33; 14 -->|bed_file| 33; 34["Junction Saturation"]; 31 -->|mapped_reads| 34; 14 -->|bed_file| 34; 35["Gene Body Coverage BAM"]; 31 -->|mapped_reads| 35; 14 -->|bed_file| 35; 36["Inner Distance"]; 31 -->|mapped_reads| 36; 14 -->|bed_file| 36; 37["Infer Experiment"]; 31 -->|mapped_reads| 37; 14 -->|bed_file| 37; 38["Read Distribution"]; 31 -->|mapped_reads| 38; 14 -->|bed_file| 38; 39["gffread"]; 32 -->|output_gtf| 39; 1 -->|output| 39; 40["StringTie merge"]; 2 -->|output| 40; 32 -->|output_gtf| 40; 41["MultiQC"]; 31 -->|output_log| 41; 37 -->|output| 41; 38 -->|output| 41; 34 -->|outputr| 41; 33 -->|stats| 41; 35 -->|outputtxt| 41; 36 -->|outputfreqtxt| 41; 42["rnaQUAST"]; 2 -->|output| 42; 1 -->|output| 42; 39 -->|output_exons| 42; 43["gffread"]; 40 -->|out_gtf| 43; 1 -->|output| 43; 44["StringTie"]; 40 -->|out_gtf| 44; 31 -->|mapped_reads| 44; 45["Filter collection"]; 3 -->|output| 45; 44 -->|transcript_expression| 45; 46["IsoformSwitchAnalyzeR"]; 2 -->|output| 46; 24 -->|integer_param| 46; 5 -->|output| 46; 45 -->|output_filtered| 46; 40 -->|out_gtf| 46; 4 -->|output| 46; 45 -->|output_discarded| 46; 43 -->|output_exons| 46; 47["IsoformSwitchAnalyzeR"]; 46 -->|switchList| 47; 48["CPAT"]; 17 -->|output_exons| 48; 47 -->|isoformNT| 48; 16 -->|output_exons| 48; 1 -->|output| 48; 49["PfamScan"]; 7 -->|output| 49; 47 -->|isoformAA| 49; 8 -->|output| 49; 9 -->|output| 49; 50["Remove beginning"]; 48 -->|orf_seqs_prob_best| 50; 51["Text reformatting"]; 50 -->|out_file1| 51; 52["Concatenate datasets"]; 6 -->|output| 52; 51 -->|outfile| 52; 53["IsoformSwitchAnalyzeR"]; 52 -->|out_file1| 53; 49 -->|output| 53; 47 -->|switchList| 53; 54["IsoformSwitchAnalyzeR"]; 52 -->|out_file1| 54; 49 -->|output| 54; 47 -->|switchList| 54;
Inputs
Input | Label |
---|---|
Input dataset collection | RNA-seq data collection |
Input dataset | Reference genome |
Input dataset | Genome annotation |
Input dataset | Control IDs |
Input parameter | Factor 02 |
Input parameter | Factor 01 |
Input dataset | CPAT header |
Input dataset | Active sites dataset |
Input dataset | Pfam-A HMM Stockholm file |
Input dataset | Pfam-A HMM library |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0 | gffread | |
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0 | gffread |
Tools
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 |
---|---|---|---|
14 | e95675763 | 2023-06-11 18:40:14 | Update plots |
13 | d3163e2b0 | 2023-06-11 12:34:56 | Update workflow |
12 | 242488cee | 2023-06-11 12:01:39 | Update workflow |
11 | 525bdefc1 | 2023-06-11 11:57:31 | Update workflow |
10 | d61cfd01e | 2023-06-11 11:52:29 | Update workflow |
9 | d8d7c1d61 | 2023-06-11 11:41:31 | Update workflow |
8 | 68b7c8719 | 2023-06-07 17:16:51 | Update workflow |
7 | e09b91c82 | 2023-06-06 03:23:06 | Add_files |
6 | fbc9e306e | 2023-05-26 18:04:55 | Add Pavan suggestions |
5 | 8cce7136d | 2023-05-24 21:17:10 | Update workflow |
4 | 4227f53c5 | 2023-05-17 14:39:03 | Update_training |
3 | 509a8973b | 2023-05-09 13:37:57 | Update workflow and bib file |
2 | c7397ec1f | 2023-05-09 13:20:38 | Modify workflow |
1 | a021922f2 | 2023-03-09 15:47:03 | Add_files |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/differential-isoform-expression/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