Genome-wide alternative splicing analysis v.2
Version 3

Version 7 (latest)

Version 6

Version 5

Version 4

Version 3

Version 2

Version 1 (earliest)

Workflow Type: Galaxy

Stable

Genome-wide alternative splicing analysis v.2

SEEK ID: https://workflowhub.eu/workflows/482?version=3

DOI: 10.48546/workflowhub.workflow.482.3

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

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