Gene read count-level batch correction in scRNA-seq?
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11 weeks ago
Jeff-Gui ▴ 10

Hi, I'm working on the integration of several scRNA-seq datasets. After trying Seurat v3 and Harmony, I realized they outputs dimension reduction matrix rather than correct read counts, therefore not suitable for some downstream analysis on gene-expression level. I wonder if there are any software that can correct batch effect on read counts.

NGS single-cell RNA seq sequencing • 419 views
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What downstream analysis are you considering?

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I think if things are not corrected on gene level, the visualization (heatmap, feature plot) of the combined dataset will be less informative. The network analysis (e.g. WGCNA) requires expression matrix input as well.

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9 weeks ago
FlMai ▴ 10

Depending on which platform you use, you could try Scanorama. The correct funktion of scanorama does correct the count matrix, also there is an external wrapper for scanpy. For comparison of different batch-correction methods have a look at A benchmark of batch-effect correction methods for single-cell RNA sequencing data

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Thanks for reminding. Harmony does not output counting matrix therefore not suitable for gene-based analysis. It seems that Seurat also has counting matrix output but my previous experience is that the "integrated" assay does not have count matrix. Does anyone know which slot it locates? Here the latest review discusses more detail. https://academic.oup.com/nar/article/49/7/e42/6125660

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