DEG Part - Ref Based RNA Seq - Transcriptomics - GTN
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/946?version=1

Inputs

ID	Name	Description	Type
Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz	Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz	gene annotation	File
Input Dataset Collection	Input Dataset Collection	Counts obtained by Feature counts	File[]
KEGG pathways to plot	KEGG pathways to plot	selected KEGG pathways to plot	File
header	header	header for annotated DESeq2 output	File

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	File
DESeq2_normalized_counts	DESeq2_normalized_counts	n/a	File
DESeq2_annotated_results_with_header	DESeq2_annotated_results_with_header	n/a	File
z_score	z_score	n/a	File
go_terms	go_terms	n/a	File
go_genes	go_genes	n/a	File
go_plot	go_plot	n/a	File
kegg_pathways	kegg_pathways	n/a	File
kegg_genes	kegg_genes	n/a	File
go_underrepresented	go_underrepresented	n/a	File
go_overrepresented	go_overrepresented	n/a	File
kegg_underrepresented	kegg_underrepresented	n/a	File
kegg_overrepresented	kegg_overrepresented	n/a	File
pathview_plot	pathview_plot	n/a	File
go_underrepresented_categories	go_underrepresented_categories	n/a	File
go_overrepresented_categories	go_overrepresented_categories	n/a	File
heatmap_log	heatmap_log	n/a	File
heatmap_zscore	heatmap_zscore	n/a	File