Workflow Type: Galaxy
Frozen
Frozen
Frozen
Frozen
Stable
This workflow correspond to the Genome-wide alternative splicing analysis training. It allows to analyze isoform switching by making use of IsoformSwitchAnalyzeR.
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
ID | Name | Description | Type |
---|---|---|---|
CPAT_header_tab | n/a | n/a |
|
GRCh38_p13_genome_fa_gz | n/a | n/a |
|
Input Dataset Collection | n/a | n/a |
|
Pfam-A_hmm_dat_gz | n/a | n/a |
|
Pfam-A_hmm_gz | n/a | n/a |
|
active_site_dat_gz | n/a | n/a |
|
gencode_v43_annotation_gtf_gz | n/a | n/a |
|
gencode_v43_lncRNA_transcripts_fa_gz | n/a | n/a |
|
gencode_v43_pc_transcripts_fa_gz | n/a | n/a |
|
gencode_v43_transcripts_fa_gz | n/a | n/a |
|
Steps
ID | Name | Description |
---|---|---|
10_Convert GTF to BED12 | n/a | n/a |
11_fastp | n/a | n/a |
12_Flatten collection | n/a | n/a |
13_RNA STAR | n/a | n/a |
14_FastQC | n/a | n/a |
15_StringTie | n/a | n/a |
16_Junction Annotation | n/a | n/a |
17_Infer Experiment | n/a | n/a |
18_Read Distribution | n/a | n/a |
19_Gene Body Coverage (BAM) | n/a | n/a |
20_Junction Saturation | n/a | n/a |
21_MultiQC | n/a | n/a |
22_Extract element identifiers | n/a | n/a |
23_MultiQC | n/a | n/a |
24_Search in textfiles | n/a | n/a |
25_Filter collection | n/a | n/a |
26_IsoformSwitchAnalyzeR | n/a | n/a |
27_IsoformSwitchAnalyzeR | n/a | n/a |
28_CPAT | n/a | n/a |
29_PfamScan | n/a | n/a |
30_Remove beginning | n/a | n/a |
31_Text reformatting | n/a | n/a |
32_Concatenate datasets | n/a | n/a |
33_IsoformSwitchAnalyzeR | n/a | n/a |
34_IsoformSwitchAnalyzeR | n/a | n/a |
Version History
Version 4 (latest) Created 25th May 2023 at 22:57 by Cristóbal Gallardo
No revision comments
Frozen
Version-4
b79e689
Version 3 Created 25th May 2023 at 22:39 by Cristóbal Gallardo
No revision comments
Frozen
Version-3
ad0a0a5
Version 2 Created 24th May 2023 at 00:22 by Cristóbal Gallardo
No revision comments
Frozen
Version-2
2010989
Version 1 (earliest) Created 17th May 2023 at 12:21 by Cristóbal Gallardo
Initial commit
Frozen
Version-1
572676e
Creators and Submitter
Creator
Submitter
Activity
Views: 4320 Downloads: 635 Runs: 0
Created: 17th May 2023 at 12:21
Annotated Properties
Topic annotations
Attributions
None