Genome-wide alternative splicing analysis
Version 4 (latest)

Version 4 (latest)

Version 3

Version 2

Version 1 (earliest)

Workflow Type: Galaxy

Stable

This workflow correspond to the Genome-wide alternative splicing analysis training. It allows to analyze isoform switching by making use of IsoformSwitchAnalyzeR.

SEEK ID: https://workflowhub.eu/workflows/472?version=4

Inputs

ID	Name	Description	Type
CPAT_header_tab	n/a	n/a	File
GRCh38_p13_genome_fa_gz	n/a	n/a	File
Input Dataset Collection	n/a	n/a	File
Pfam-A_hmm_dat_gz	n/a	n/a	File
Pfam-A_hmm_gz	n/a	n/a	File
active_site_dat_gz	n/a	n/a	File
gencode_v43_annotation_gtf_gz	n/a	n/a	File
gencode_v43_lncRNA_transcripts_fa_gz	n/a	n/a	File
gencode_v43_pc_transcripts_fa_gz	n/a	n/a	File
gencode_v43_transcripts_fa_gz	n/a	n/a	File

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