Differential Expression

Now that we have finished mapping our reads we are ready to perform differential expression.

The following step applies for simple screens or 1-dimensional screens which are generally of the form:

sample_low_1
sample_low_2
sample_high_1
sample_high_2

Note: More complicated schemas For more complicated schemas I recommend using DESeq2 for sgRNA expression then aggregating gene-level information with sgagg.

Installation

For this analysis we will need to use crispr_screen. We can install it easily with the rust package manager cargo

cargo install crispr_screen

Usage

To run our analysis we just use the following command:

crispr_screen test \
  -i mapping.tab \
  -c sample_low_1 sample_low_2 \
  -t sample_high_1 sample_high_2

This will create 2 output files results.gene_results.tab and results.sgrna_results.tab which reflect the differential expression at the gene and sgrna level respectively.

More Information

This will perform the default enrichment analysis - but for more details or alternative analysis methods check out the crispr_screen documentation.