Quick Start Guide

Complete differential splicing analysis in 5 steps: from data upload to primer design

1

Upload Files

2

Set Parameters

3

Run Analysis

4

View Results

5

Validation & Primers

01

Upload rMATS Result Files

Upload standard output files (.txt format) from rMATS software. The system will automatically identify event types.

Supported files: SE.MATS.JC.txt, A3SS.MATS.JC.txt, A5SS.MATS.JC.txt, RI.MATS.JC.txt, MXE.MATS.JC.txt

Upload method: Drag and drop files into the dashed box, or click to select. Multiple selection is supported.

Tip: Click the "Load Example" button to automatically load test data and experience the full workflow.

Drag files here, or click to select Supports .txt / .tsv / .csv formats

02

Select Reference Genome & Parameters

Select the study species and the corresponding reference genome annotation file (should match the annotation used during splicing analysis). The system will automatically match the FASTA sequence.

Species selection: Supports Human (Homo sapiens) and Mouse (Mus musculus)

Core parameters: FDR threshold (default 0.05), |ΔPSI| threshold (default 0.1), Min Junction Count (MiniJC, default 10)

Note: MiniJC is not part of standard rMATS output. Simply put, the average of IJC/SJC across two samples must not both be below the threshold (to exclude identical trends), and neither Sample 1 nor Sample 2 counts should simultaneously fall below the threshold (to exclude low counts due to sample factors).

FDR Threshold / |ΔPSI| Threshold / Min Junction Count Adjust parameters by dragging sliders or entering values directly

03

Run Analysis & View Overview

Click the "Start Analysis" button to submit the task. The system will process it automatically and generate results.

Run: Click "Start Analysis" to send the task to background processing.

Overview: Automatically redirects to "Results Overview" upon completion to view statistical charts such as event type distribution and NMD status.

Download: Download Excel result files and GB sequence files from the sidebar.

Event Type Distribution / NMD Status / Top 10 Genes by Event Count Automatically generates statistical charts and enrichment analysis results

04

View Event List & Visualization

Browse all significant differential splicing events on the "Event List" page. Click the "Sequence" button to enter the genome browser.

Event List: Filter by type, NMD status, and match status. Click a row to view details.

Visualization: Click the "Sequence" button to view the splicing event in the genome browser visualization.

Export: In the sequence view, EXON refers to the exon splicing view, while TRAN refers to the genomic view (mainly used for RI validation design). The focused view shows the splicing change region plus 5000bp upstream and downstream (meeting most splicing analysis requirements).

Genome Browser View - Exon/Intron Visualization Click "Sequence" button to view event details

05

Change Validation & Primer Design

On the "Visualization" page, design validation primers based on the splicing event type. Switching between exon/intron views is supported.

SE (Skipped Exon): In EXON view, design primers on the flanking exons of the SKIP_EXON. IJC represents the full length between primers (including the skipped exon), while SJC represents the shorter product after skipping the exon.

RI (Retained Intron): In TRAN view, design primers on the flanking exons of the RETAINED_INTRON. IJC represents the longer fragment containing the retained intron, while SJC represents the shorter fragment without the intron.

MXE (Mutually Exclusive Exons): Combine MXE_Exon1_Candidate or MXE_Exon2_Candidate with forward/reverse primers respectively, or design primers outside both exons, distinguishing them by product length.

Primer Design Illustration · Exon/Intron View Click "Sequence" to enter genome browser for primer design

Analysis Environment & Input Files

Study Species*

Reference Genome Annotation (GTF)*

Please select reference genome annotation

Associated Genome Sequence (FASTA)

Waiting for selection...

Automatically matches corresponding reference sequence based on selected GTF

Analysis Software

Output Format Adaptation: Please upload SE.MATS.JC.txt A3SS.MATS.JC.txt etc. from the standard rMATS output directory

Input Files (Junction Counts)*

Drag files here, or click to select files
Supports .txt formats. Multiple files can be selected at once.

Unsupported file format. Please upload .txt / .tsv / .csv files.

No files added yet

rMATS Core Parameters

FDR Threshold

|ΔPSI| Threshold

Min Junction Count

Notification

Notification Email (Optional) Leave empty to skip. We'll automatically email you when the analysis completes.

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Total Differential Events

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Related Genes

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OK Matched Events

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NMD Targets

Analysis Parameters The settings this run was submitted with

Event Type Distribution

NMD Status Distribution

Top 10 Genes by Event Count

Event Type × NMD Status

Differential Event List

Loading...

#	Event Type	Gene	IJC_S1	SJC_S1	IJC_S2	SJC_S2	FDR	ΔPSI	NMD Status	Actions
Please run analysis first

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Event Details

Basic Information

Event ID-

Event Type-

Gene-

NMD Status-

Match Status-

FDR-

|ΔPSI|-

Transcript ID-

Coordinate Information

exonStart_0base-

exonEnd-

riExonStart_0base-

riExonEnd-

1stExonStart-

1stExonEnd-

2ndExonStart-

2ndExonEnd-

shortES-

shortEE-

longExonStart-

longExonEnd-

flankingES-

flankingEE-

upstreamES-

upstreamEE-

downstreamES-

downstreamEE-

Sequence Information

Reference CDS

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Reference Protein

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Alternative CDS

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Alternative Protein

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Diff CDS

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Diff Protein

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Genome Browser View
Please click the "Sequence" button in the Differential Event List to view

BioSpliceView

RNA Splicing Differential Analysis Visualization Platform | Differential Splicing Event Analysis Tool Based on rMATS | Genome Browser View

v1.5.3 Python Flask BioPython

Platform Core Features

① Coding sequences and protein sequences after splicing changes

② Prediction of whether nonsense-mediated mRNA decay (NMD) occurs after the change

③ Intuitive visualization of splicing change regions to facilitate primer and minigene design

Citation & Links

GitHub Repository: https://github.com/rennmeng/BioSpliceView

bio.tools Registry: https://bio.tools/BioSpliceView

Version Update Log

v1.5.3

Fixed: Streamlined functionality by removing GO and KEGG analyses

v1.5.1

Fixed: Fix the bugs in the processing of A5SS and A3SS sequences

v1.3.10

Added: Job ID display at top, parallel stepper clicking, current step highlighting

v1.3.9

Fixed: Confirmation dialog style optimization, direct use of color variables

v1.3.6

Added: Added "Download List" function to enrichment analysis table for one-click export of pathway-related genes

v1.3.0

Feature: Integrated genome visualization browser (JBrowse), supporting differential event list and sequence detail viewing

Contact Us

If you have any questions or suggestions, please feel free to contact us.
rennmeng@smail.nju.edu.cn

Job History

Enter Job ID to load completed analysis results (within 48h)

Quick Start Guide

Upload rMATS Result Files

Select Reference Genome & Parameters

Run Analysis & View Overview

View Event List & Visualization

Change Validation & Primer Design

Differential Event List

Event Details

BioSpliceView

Contact Us

Job History

Missing Event Types Detected