Genome-wide alternative splicing analysis v.2
Version 1

Workflow Type: Galaxy

Stable

Genome-wide alternative splicing analysis v.2.

SEEK ID: https://workflowhub.eu/workflows/482?version=1

Inputs

ID	Name	Description	Type
Active sites dataset	n/a	n/a	File
CPAT header	n/a	n/a	File
Genome annotation	n/a	n/a	File
Pfam-A HMM Stockholm file	n/a	n/a	File
Pfam-A HMM library	n/a	n/a	File
Protein coding transcripts	n/a	n/a	File
RNA-seq data collection	n/a	n/a	File
Reference genome	n/a	n/a	File
lncRNA transcripts	n/a	n/a	File

ID	Name	Description
10_fastp	n/a	n/a
11_Flatten collection	n/a	n/a
12_RNA STAR	n/a	n/a
13_FastQC	n/a	n/a
14_Concatenate datasets	n/a	n/a
15_MultiQC	n/a	n/a
16_Text reformatting	n/a	n/a
17_Cut	n/a	n/a
18_Sort	n/a	n/a
19_Unique	n/a	n/a
20_RNA STAR	n/a	n/a
21_Infer Experiment	n/a	n/a
22_Junction Saturation	n/a	n/a
23_Gene Body Coverage (BAM)	n/a	n/a
24_Read Distribution	n/a	n/a
25_Junction Annotation	n/a	n/a
26_StringTie	n/a	n/a
27_MultiQC	n/a	n/a
28_StringTie merge	n/a	n/a
29_StringTie	n/a	n/a
30_gffread	n/a	n/a
31_Extract element identifiers	n/a	n/a
32_Search in textfiles	n/a	n/a
33_Filter collection	n/a	n/a
34_IsoformSwitchAnalyzeR	n/a	n/a
35_IsoformSwitchAnalyzeR	n/a	n/a
36_CPAT	n/a	n/a
37_PfamScan	n/a	n/a
38_Remove beginning	n/a	n/a
39_Text reformatting	n/a	n/a
40_Concatenate datasets	n/a	n/a
41_IsoformSwitchAnalyzeR	n/a	n/a
42_IsoformSwitchAnalyzeR	n/a	n/a
9_Convert GTF to BED12	n/a	n/a