Workflow Type: Galaxy
Open
Frozen
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial DEG Part - Ref Based RNA Seq - Transcriptomics - GTN, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle
Tutorial Contributor(s): Helena Rasche
Workflow Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle
Inputs
ID | Name | Description | Type |
---|---|---|---|
Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz | Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz | gene annotation |
|
Input Dataset Collection | Input Dataset Collection | Counts obtained by Feature counts |
|
KEGG pathways to plot | KEGG pathways to plot | selected KEGG pathways to plot |
|
header | header | header for annotated DESeq2 output |
|
Steps
ID | Name | Description |
---|---|---|
4 | Extract samples' name | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
5 | Compute gene length | toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2 |
6 | Extract groups | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
7 | Change Case | ChangeCase |
8 | Tag elements with groups | __TAG_FROM_FILE__ |
9 | Differential Analysis | toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2 |
10 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
11 | Annotate DESeq2/DEXSeq output tables | toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0 |
12 | Table Compute | toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 |
13 | Cut | Cut1 |
14 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
15 | Table Compute | toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 |
16 | Change Case | ChangeCase |
17 | Filter | Filter1 |
18 | goseq | toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 |
19 | goseq | toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 |
20 | Cut | Cut1 |
21 | Filter | Filter1 |
22 | Filter | Filter1 |
23 | Filter | Filter1 |
24 | Filter | Filter1 |
25 | Filter | Filter1 |
26 | Pathview | toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0 |
27 | Join two Datasets | join1 |
28 | Group | Grouping1 |
29 | Group | Grouping1 |
30 | Cut | Cut1 |
31 | heatmap2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0 |
32 | heatmap2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
DESeq2_plots | DESeq2_plots | n/a |
|
DESeq2_normalized_counts | DESeq2_normalized_counts | n/a |
|
DESeq2_annotated_results_with_header | DESeq2_annotated_results_with_header | n/a |
|
z_score | z_score | n/a |
|
go_terms | go_terms | n/a |
|
go_genes | go_genes | n/a |
|
go_plot | go_plot | n/a |
|
kegg_pathways | kegg_pathways | n/a |
|
kegg_genes | kegg_genes | n/a |
|
go_underrepresented | go_underrepresented | n/a |
|
go_overrepresented | go_overrepresented | n/a |
|
kegg_underrepresented | kegg_underrepresented | n/a |
|
kegg_overrepresented | kegg_overrepresented | n/a |
|
pathview_plot | pathview_plot | n/a |
|
go_underrepresented_categories | go_underrepresented_categories | n/a |
|
go_overrepresented_categories | go_overrepresented_categories | n/a |
|
heatmap_log | heatmap_log | n/a |
|
heatmap_zscore | heatmap_zscore | n/a |
|
Version History
8.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche
Added/updated 4 files
Open
master
13c5f15
22.0 (earliest) Created 25th Jun 2024 at 11:25 by Helena Rasche
Added/updated 4 files
Frozen
22.0
c080d1f
Creators and Submitter
Creators
Not specifiedSubmitter
Discussion Channel
License
Activity
Views: 726 Downloads: 234
Created: 25th Jun 2024 at 11:24
Last updated: 5th Jul 2024 at 14:24
Tags
Attributions
None