--count-table	Provide a tab-separated count table. Each line in the table should include sgRNA name (1st column), target gene (2nd column) and the read count in each sample (3rd and subsequent columns).
--design-matrix	Provide a design matrix (For instructions to generate the design matrix, see Box 3), either as a file name or a quoted string of the design matrix. An example of design matrix is shown in Table 5. The row of the design matrix must match the order of the samples in the count table (if --include-samples is not specified), or the order of the samples is specified by the --include-samples option.
--norm-method	{none, median, total, control} Method for normalization, including “none” (no normalization), “median” (median normalization, default), “total” (normalization by total read counts), “control” (normalization by control sgRNAs specified by the --control-sgrna option).
--control-sgrna	A list of control sgRNAs.
--output-prefix	The prefix of the output file(s). Default is “sample1”.