-k	Count table (Table 4, Step 7Aiii), provide a tab-separated count table. Each line in the table should include sgRNA name (1st column), target gene (2nd column) and read counts (3rd column) in each sample.
-t	Sample label or sample index (0 as the first sample according to python standard) in the count table that are to be treated as treatment experiments, separated by comma (,). If sample labels are provided (rather than a sample index), the labels must match the labels in the first line of the count table. This parameter is required, which means at least one sample should be assigned to this parameter.
-c	Sample label or sample index in the count table that are to be treated as control experiments, separated by comma (,). If no samples are specified by this parameter, controls will be defined as all the samples not specified by the -t parameter. This parameter is required, which means at least one sample should be assigned to this parameter.”
-n	The prefix of the output files.
--remove-zero	Remove sgRNAs whose mean value is zero in control, treatment, both control/treatment, or any control/treatment sample. Default: both (remove those sgRNAs that are zero in both control and treatment samples).
--remove-zero-threshold sgRNA normalized count threshold to be considered removed in the --remove-zero option. Default 0.