SinQC – Quality Control of Single-cell RNA-Seq

Single-cell RNA-seq (scRNA-seq) is emerging as a promising technology for profiling cell-to-cell variability in cell populations. However, the combination of technical noise and intrinsic biological variability makes detecting technical artifacts in scRNA-seq samples particularly challenging. Proper detection of technical artifacts is critical to prevent spurious results during downstream analysis.

Researchers from the Morgridge Institute for Research have devloped ‘Single-cell RNA-seq Quality Control’ (SinQC), a method and software tool to detect technical artifacts in scRNA-seq samples by integrating both gene expression patterns and data quality information. They apply SinQC to nine different scRNA-seq datasets, and show that SinQC is a useful tool for controlling scRNA-seq data quality.

rna-seq

Technical artifacts detected by SinQC (FPR < 5%) in a highly heterogeneous dataset containing a mixture of 11 cell types.

Availability – SinQC software and documents are available at http://www.morgridge.net/SinQC.html

ContactPJiang@morgridge.org or RStewart@morgridge.org

Jiang P, Thomson JA, Stewart R. (2016) Quality Control of Single-cell RNA-seq by SinQC. Bioinformatics [Epub ahead of print]. [article]

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