Workflows
These workflows are associated with Genome-wide alternative splicing analysis
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.
Genome-wide alternative splicing analysis: human
Cristóbal Gallardo Alba
Last updated Jun 11, 2023
Launch in Tutorial Mode
License:
CC-BY-SA-4.0
Tests: ✅
Results: Not yet automated
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;
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: