Last updated: 2018-12-02

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Crop-seq

Exploratory Analysis & DESeq2 from Alan (11/07/2018)

Exploratory Analysis from Siwei (11/19/2018)

Quality_metrics

In this workflow, I show how to process the raw FastQ files into count matrices representing UMI. We use the CellRanger toolkit to perform the processing. Then, we load the UMI matrices into R and perform exploratory analysis. We find that 2200+ cells have exactly 1 guide RNA and ~400 cells have zero. For the top expressed guide RNA, we perform differential expression analysis using DESeq2.


This reproducible R Markdown analysis was created with workflowr 1.1.1