rnaseq-de/main
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Tests This workflow can only work on an experimental setup with exactly 2 conditions. It takes two collections of count tables as input and performs differential expression analysis. Additionally it filters for DE genes based on adjusted p-value and log2 fold changes thresholds. It also generates informative plots.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Adjusted p-value threshold | Adjusted p-value threshold | Adjusted p-value threshold to call genes as differentially expressed. If not set, default 0.05 is used. |
|
| Count files have header | Count files have header | Usually, count files generated from featureCounts tool have a header line whereas count files from RNA-STAR do not have. |
|
| Counts from changed condition | Counts from changed condition | Counts from experimental condition or changed condition. For eg. counts from treatment or knockdown samples. |
|
| Counts from reference condition | Counts from reference condition | Counts from reference condition or base condition. For eg. counts from untreated or wildtype samples. |
|
| Gene Annotaton | Gene Annotaton | The same annotation GTF used for mapping and counting |
|
| log2 fold change threshold | log2 fold change threshold | log2 fold change threshold to filter for highly regulated genes. If not set, default 1.0 is used. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1 |
| 7 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 8 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
| 9 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 10 | Differential Analysis | toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0 |
| 11 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 12 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 13 | Annotate DESeq2/DEXSeq output tables | toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0 |
| 14 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 15 | Annotate DESeq2 table | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 |
| 16 | Parse parameter value | param_value_from_file |
| 17 | Filter with p-adj threshold | Filter1 |
| 18 | Generate Valcanot plot of DE genes | toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6 |
| 19 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 20 | Filter with log2 FC threshold | Filter1 |
| 21 | Join two Datasets | join1 |
| 22 | Cut | Cut1 |
| 23 | Generate Heatmap of counts | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1 |
| 24 | Generate Heatmap of Z-scores | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| DESeq2 Plots | DESeq2 Plots | n/a |
|
| DESeq2 Normalized Counts | DESeq2 Normalized Counts | n/a |
|
| Annotated DESeq2 results table | Annotated DESeq2 results table | n/a |
|
| Volcano Plot of DE genes | Volcano Plot of DE genes | n/a |
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| Significantly differentially expressed genes | Significantly differentially expressed genes | n/a |
|
| Heatmap of log transformed normalized counts | Heatmap of log transformed normalized counts | n/a |
|
| Heatmap of Z-scores | Heatmap of Z-scores | n/a |
|
Version History
v0.1 (earliest) Created 13th Nov 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1d0491c7
Creators and SubmitterLicense
Activity
Views: 90 Downloads: 28 Runs: 0
Created: 13th Nov 2024 at 03:02
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https://orcid.org/0000-0002-5192-126X
Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
Teams: usegalaxy-eu
Organizations: Albert-Ludwigs-Universität Freiburg
https://orcid.org/0000-0002-5192-126X
Advanced Teams list for this Workflow with search and filtering
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
