Workflow Type: Galaxy
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This workflow correspond to the Genome-wide alternative splicing analysis training. It allows to analyze isoform switching by making use of IsoformSwitchAnalyzeR.
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 |
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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
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Version-4
b79e689
Version 3 Created 25th May 2023 at 22:39 by Cristóbal Gallardo
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Version-3
ad0a0a5
Version 2 Created 24th May 2023 at 00:22 by Cristóbal Gallardo
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Version-2
2010989
Version 1 (earliest) Created 17th May 2023 at 12:21 by Cristóbal Gallardo
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Version-1
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Created: 17th May 2023 at 12:21
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