CRISPR Single Cell Screen DropSeq Genotyping Pipeline

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The input to the data analysis pipeline is a DropSeq cDNA fastq file and a DropSeq gRNA fastq file. The details of the pipeline are outlined in these slides File:Computational Pipeline.pptx. The pipeline outputs a RNA-Seq count matrix with the genes as rows and cells as columns. The cells are each labeled with the gRNA knockout that was detected, if any. Each count represents a detected mRNA transcript. The pipeline also outputs various summary statistics and can perform some sanity checks.

The python code and shell scripts are attached in this repository: File:DropSeq gRNA Genotyping.zip