Recently this paper by Ilicic et al. suggested a method for assessing the quality of individual cells in a single-cell RNA-seq experiment. The basic idea is to extract various biological and technical features from each the reads for each cell, then use PCA with outlier detection or a SVM to classify cells as “high” or “low” quality. There are two pieces of software associated with the paper: cellity, an R package that performs the classification and Celloline, a Python script that performs alignment, summarisation and extraction of alignment statistics such as the number of reads aligned to exons, introns, intergenic regions etc.

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Luke Zappia

Bioinformatician in training

PhD student

Australia