Workflow Type: Galaxy
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Genome-wide alternative splicing analysis v.2
Inputs
ID | Name | Description | Type |
---|---|---|---|
Active sites dataset | n/a | Active sites dataset. |
|
CPAT header | n/a | Galaxy compatible CPAT header. |
|
Control IDs | n/a | IDs of control sequences, corresponding to filenames. |
|
Genome annotation | n/a | Reference genome annotation in GTF format. |
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Pfam-A HMM Stockholm file | n/a | Stockholm file. |
|
Pfam-A HMM library | n/a | HMM library. |
|
RNA-seq data collection | n/a | Collection of paired-end RNA-seq datasets. |
|
Reference genome | n/a | Genome reference in FASTA format. |
|
Steps
ID | Name | Description |
---|---|---|
10_Flatten collection | n/a | n/a |
11_fastp | n/a | n/a |
12_Search in textfiles | n/a | n/a |
13_Search in textfiles | n/a | n/a |
14_Convert GTF to BED12 | n/a | n/a |
15_FastQC | n/a | n/a |
16_gffread | n/a | n/a |
17_gffread | n/a | n/a |
18_Gene BED To Exon_Intron_Codon BED | n/a | n/a |
19_MultiQC | n/a | n/a |
20_Search in textfiles | n/a | n/a |
21_Text reformatting | n/a | n/a |
22_Concatenate datasets | n/a | n/a |
23_Text reformatting | n/a | n/a |
24_Text reformatting | n/a | n/a |
25_Cut | n/a | n/a |
26_Parse parameter value | n/a | n/a |
27_Parse parameter value | n/a | n/a |
28_Text reformatting | n/a | n/a |
29_Parse parameter value | n/a | n/a |
30_RNA STAR | n/a | n/a |
31_Concatenate datasets | n/a | n/a |
32_Text reformatting | n/a | n/a |
33_Cut | n/a | n/a |
34_Sort | n/a | n/a |
35_Unique | n/a | n/a |
36_RNA STAR | n/a | n/a |
37_Inner Distance | n/a | n/a |
38_Infer Experiment | n/a | n/a |
39_StringTie | n/a | n/a |
40_Gene Body Coverage (BAM) | n/a | n/a |
41_Junction Annotation | n/a | n/a |
42_Read Distribution | n/a | n/a |
43_Junction Saturation | n/a | n/a |
44_gffread | n/a | n/a |
45_StringTie merge | n/a | n/a |
46_MultiQC | n/a | n/a |
47_rnaQUAST | n/a | n/a |
48_StringTie | n/a | n/a |
49_gffread | n/a | n/a |
4_Input parameter | n/a | n/a |
50_Filter collection | n/a | n/a |
51_IsoformSwitchAnalyzeR | n/a | n/a |
52_IsoformSwitchAnalyzeR | n/a | n/a |
53_CPAT | n/a | n/a |
54_PfamScan | n/a | n/a |
55_Remove beginning | n/a | n/a |
56_Text reformatting | n/a | n/a |
57_Concatenate datasets | n/a | n/a |
58_IsoformSwitchAnalyzeR | n/a | n/a |
59_IsoformSwitchAnalyzeR | n/a | n/a |
5_Input parameter | n/a | n/a |
Version History
Version 7 (latest) Created 11th Jun 2023 at 20:17 by Cristóbal Gallardo
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Version 4 Created 11th Jun 2023 at 12:57 by Cristóbal Gallardo
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Version 3 Created 11th Jun 2023 at 12:53 by Cristóbal Gallardo
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Version 2 Created 7th Jun 2023 at 17:10 by Cristóbal Gallardo
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Version 1 (earliest) Created 25th May 2023 at 23:01 by Cristóbal Gallardo
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Views: 6457 Downloads: 1279 Runs: 0
Created: 25th May 2023 at 23:01
Last updated: 7th Jun 2023 at 17:00
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