LeafCutter2 Pipeline

Execution Mode

Most users should start with Local. Switch to Quest Slurm only if you have an account on Northwestern's Quest cluster.

Input Source

Upload Files GTEx Portal (V8) Zebrafish (Public Projects)

Pipeline Inputs

STAR SJ.out.tab files

Select one or more STAR splice-junction output files.

Samples TSV (optional)

Two-column file: sample <TAB> condition

GTEx V8 Tissues

Select one or more GTEx tissues. Junction data will be downloaded from the GTEx Portal (~4 GB total on first run) and converted to per-sample BED files.

Tissues (hold Ctrl/Cmd for multi-select)

Loading tissue list...

Max Samples per Tissue

Limit the number of samples used per tissue. Set to 0 to use all available samples. A value like 50–100 is useful for quick test runs.

Zebrafish End-to-End (Quest)

3-step pipeline: QC & Trim → STAR Alignment → LeafCutter2 Analysis. Enter project IDs, run QC first, review reports, then proceed to alignment and analysis.

Project IDs (comma-separated)

QC Job ID (required for Step 2)

Alignment Job ID (required for Step 3)

LC2 Job ID (optional, for Step 4 cross-ref)

POISEN PE list (path on Quest repo)

LongORF PTC TSV (path on Quest repo)

Timepoints for Step 3 (optional; default all)

Run Step 2 first, then load timepoints.

Max Runs (optional) STAR Threads Zebrafish Genome FASTA (path on Quest repo) Zebrafish GTF (path on Quest repo) GTF gene type tag GTF transcript type tag GTF gene name/id tag GTF transcript name/id tag

This source is Quest-only in v1 (mode must be Slurm).

Parameters

Run Prefix

Min Reads

Max Intron Len

Quest Slurm Settings

Quest Username (NetID)

Quest Host

Slurm Account

Partition

Leaf_Cutter Repo Path on Quest Remote Job Directory Root Remote Junction File List (skip upload)

If your data is already on Quest, provide the path to the junction file list here.

LeafCutter2 Pipeline

Execution Mode

Input Source

Pipeline Inputs

GTEx V8 Tissues

Zebrafish End-to-End (Quest)

Parameters

Quest Slurm Settings

Job Status

Results

UP Junction PSI Heatmap (top candidates)

PSI Correlation with Developmental Time

NMD Feature Distributions

Top Poison-Exon Candidates

PSI heatmap (top candidates by FDR)

PSI vs developmental time (top candidates)

Spearman \u03c1 distribution

LC2 concordance

Ranked POISEN PE candidates

Recent Jobs

Welcome to LeafCutter2

1. Where will you run the pipeline?

2. Configure

3. Pick an input source

4. You're all set

LeafCutter2 Pipeline

Execution Mode

Input Source

Pipeline Inputs

GTEx V8 Tissues

Zebrafish End-to-End (Quest)

Parameters

Quest Slurm Settings

Job Status

Results

UP Junction PSI Heatmap (top candidates)

PSI Correlation with Developmental Time

NMD Feature Distributions

Top Poison-Exon Candidates

PSI heatmap (top candidates by FDR)

PSI vs developmental time (top candidates)

Spearman \u03c1 distribution

LC2 concordance

Ranked POISEN PE candidates

Recent Jobs