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Single Cell RNA-Seq FAQ

What tools do you use in Basepair's single cell pipeline?
Our single cell RNA-seq pipeline uses: 1. UMI-tools for extracting barcodes 2. the STAR tool for alignment 3. fastp for QC 4. Seurat for clustering and ...
Mon, 26 Oct, 2020 at 10:54 AM
Can I upload two samples of single cell RNA-seq data (treatment and control) and compare them?
Basepair has a pipeline called "Single cell RNA-seq integrate" that allows users to upload multiple replicates to both the treatment and control g...
Mon, 26 Oct, 2020 at 10:57 AM
How do you account for technical variability? Does the program fit for mean variance trend, test for non zero biological variability, or deconvolution based normalization?
Gene expression is first normalized to account for total expression within each cell, then a log transform is applied. To select genes for downstream unsupe...
Mon, 26 Oct, 2020 at 11:01 AM
Do you check the relationship between nUMI vs nGenes plot? Do you have a specific threshold in this graph?
We do not explicitly check the relationship between nUMI and nGenes, but we do provide thresholds to remove genes with too high or too low nUMI or nGenes. I...
Mon, 26 Oct, 2020 at 11:05 AM