Genome-wide alternative splicing analysis
Version 3

Version 4 (latest)

Version 3

Version 2

Version 1 (earliest)

Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
Scalable: Galaxy can run ...

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.

Click and drag the diagram to pan, double click or use the controls to zoom.

SEEK ID: https://workflowhub.eu/workflows/472?version=3

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