MaGIC QC & Normalization Tool
MaGIC QC & Normalization Tool
Welcome to the QC & Normalization Tool by the Molecular and Genomics Informatics Core (MaGIC).
What This Tool Does
This is the front door of the MaGIC bulk-expression pipeline. Upload a raw count matrix and sample metadata, inspect the quality of your samples, flag outliers, and export a normalized expression matrix in the exact format the downstream MaGIC tools (DEG, Volcano, Heatmap, Dimensionality Reduction) expect.
How to Use This Tool
- Data Input. Upload your raw count matrix and sample metadata (and, optionally, a gene-info table for biotype QC and TPM). Confirm the sample IDs match, then Submit.
- QC Overview. Review library sizes, detected genes, biotype composition, sample–sample correlation, and expression distributions.
- PCA / Outlier. Project samples onto principal components, colour by metadata, and flag outliers by Mahalanobis distance.
- Normalization. Pick a normalization method, compare before/after distributions, and download the normalized matrix + per-sample QC metrics.
Required Input Data Formats
Raw Count Matrix
- File format: CSV or TSV
- Rows: genes (one gene per row)
- Columns: samples (one sample per column)
- First column: gene identifiers
- Values: raw (un-normalized) integer counts
GeneID, Control1, Control2, Treatment1 ENSG0001, 149, 122, 218 ENSG0002, 409, 151, 46
Sample Metadata
- File format: CSV or TSV
- Rows: samples (one sample per row)
- First column: sample names — must match matrix column names
- Additional columns: any annotation (condition, batch, time, ...)
Sample, Group, Batch Control1, Control, B1 Control2, Control, B2
Gene Info Table (optional)
- Maps gene IDs to symbol, biotype, and length
- Biotype column enables the biotype-composition QC plot
- Length column (in bp) enables TPM normalization
GeneID, Symbol, Biotype, Length ENSG0001, GENE1, protein_coding, 2400 ENSG0002, GENE2, lncRNA, 1800
Input Data
Raw Count Matrix
Salmon Quant Files
Sample Metadata
Gene Info (optional)
Explore the tool with a built-in demo dataset.
Demo: 300 genes across 9 samples in 3 groups (Control / Treatment / Sham), with batch + time metadata and a gene-info table. Sham3 is a deliberately low-depth sample.
QC Options
Options change with the selected plot.
X axis
Y axis
Legend
PCA Options
Options change with the selected plot.