GTN_differential_isoform_expression

transcriptomics-differential-isoform-expression/main-workflow

Author(s)
Cristobal Gallardo, Lucille Delisle
Version
3
Last updated
Sep 12, 2024
License
MIT
Tags

Features
Tutorial
Genome-wide alternative splicing analysis
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00236
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
output
report_json
output
output
output_paired_coll
bed_file
output
output
output
output
text_file
splice_junctions
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
output
output
output_paired_coll
outfile
output
mapped_reads
mapped_reads
bed_file
mapped_reads
bed_file
mapped_reads
bed_file
mapped_reads
bed_file
mapped_reads
bed_file
mapped_reads
bed_file
output
output_gtf
output_gtf
output
output_log
reads_per_gene
output
outputr
outputtxt
outputfreqtxt
output
stats
out_gtf
mapped_reads
output
out_gtf
signal_unique_str2
signal_unique_str1
out_gtf
out_gtf
output
signal_unique_str2
signal_unique_str1
out_gtf
signal_unique_str2
signal_unique_str1
out_gtf
output
output
output_exons
transcript_expression
tmap_output
output
output
transcript_expression
output
output_discarded
out_gtf
output_filtered
output_exons
switchList
output
isoformAA
output
output
output_exons
isoformNT
output_exons
output
orf_seqs_prob_best
out_file1
out_file1
output
out_file1
out_file1
output
switchList
out_file1
output
switchList
ℹ️ Input Collection
RNA-seq data collection
ℹ️ Input Dataset
Genome annotation
ℹ️ Input Dataset
Reference genome
ℹ️ Input Dataset
Pfam-A HMM library
ℹ️ Input Dataset
Pfam-A HMM Stockholm file
ℹ️ Input Dataset
Active sites dataset
ℹ️ Input Dataset
CPAT header
Flatten collection
fastp
Convert GTF to BED12
Search in textfiles
Search in textfiles
FastQC
gather fastp reports
RNA STAR
Gene BED To Exon/Intron/Codon BED
gffread
gffread
gather FastQC reports
Concatenate datasets
Compute
Filter
Sort
Cut
Text reformatting
Text reformatting
Sort
Unique lines
RNA STAR
StringTie
Infer Experiment
Gene Body Coverage BAM
Junction Saturation
Junction Annotation
Inner Distance
Read Distribution
StringTie merge
gffread
MultiQC
StringTie
GffCompare
Plot a transcript in intron
gffread
Plot ADD3
Plot ADD3 zoomed
rnaQUAST
Extract element identifiers
Filter
Search in textfiles
Filter collection
IsoformSwitchAnalyzeR
IsoformSwitchAnalyzeR
PfamScan
CPAT
Cut
Add column
Remove beginning
Concatenate datasets
IsoformSwitchAnalyzeR
IsoformSwitchAnalyzeR
Output
consequencesSummary
Output
consequencesEnrichment
Output
splicingEnrichment
Output
mostSwitching
Output
splicingSummary

Inputs

Input Label
Input dataset collection RNA-seq data collection
Input dataset Genome annotation
Input dataset Reference genome
Input dataset Pfam-A HMM library
Input dataset Pfam-A HMM Stockholm file
Input dataset Active sites dataset
Input dataset CPAT header

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5 IsoformSwitchAnalyzeR

Tools

Tool Links
Cut1
Filter1
Remove beginning1
__FILTER_FROM_FILE__
__FLATTEN__
cat1
gene2exon1
sort1
toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.5+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/pfamscan/pfamscan/1.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0 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
  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
16 21737f95d 2024-09-06 08:43:16 update slides - workflow - tutorial conclusion
15 a04d2d7a8 2024-09-05 12:45:49 update end of tutorial + results
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