Workflow Type: Galaxy
Stable

Genome-wide alternative splicing analysis v.2

Inputs

ID Name Description Type
Active sites dataset n/a Active sites dataset.
  • File
CPAT header n/a Galaxy compatible CPAT header.
  • File
Control IDs n/a IDs of control sequences, corresponding to filenames.
  • File
Genome annotation n/a Reference genome annotation in GTF format.
  • File
Pfam-A HMM Stockholm file n/a Stockholm file.
  • File
Pfam-A HMM library n/a HMM library.
  • File
RNA-seq data collection n/a Collection of paired-end RNA-seq datasets.
  • File
Reference genome n/a Genome reference in FASTA format.
  • File

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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Frozen Version-4 820ad68

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Frozen Version-3 72a6796

Version 2 Created 7th Jun 2023 at 17:10 by Cristóbal Gallardo

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Frozen Version-2 c6f2e2d

Version 1 (earliest) Created 25th May 2023 at 23:01 by Cristóbal Gallardo

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Frozen Version-1 746fae8
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Views: 2000

Created: 25th May 2023 at 23:01

Last updated: 7th Jun 2023 at 17:00

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