CRISPRessoCompare Parameters
Sample Name
-n, --name
Help: Output name of the report (default: the name is obtained from the filename of the fastq file/s used in input)
Type: str
Output Folder
-o, --output_folder
Help: Output folder to use for the analysis (default: current folder)
Type: str
Verbosity
-v, --verbosity
Help: Verbosity level of output to the console (1-4) 4 is the most verbose
Type: int
Default: 3
Min Frequency Alleles Around Cut To Plot
--min_frequency_alleles_around_cut_to_plot
Help: Minimum %% reads required to report an allele in the alleles table plot.
Type: float
Default: 0.2
Zip Output
--zip_output
Help: If set, the output will be placed in a zip folder.
Type: bool
Default: False
Max Rows Alleles Around Cut To Plot
--max_rows_alleles_around_cut_to_plot
Help: Maximum number of rows to report in the alleles table plot.
Type: int
Default: 50
Suppress Report
--suppress_report
Help: Suppress output report
Type: bool
Default: False
Place Report In Output Folder
--place_report_in_output_folder
Help: If true, report will be written inside the CRISPResso output folder. By default, the report will be written one directory up from the report output.
Type: bool
Default: False
Debug
--debug
Help: Show debug messages
Type: bool
Default: False
Crispresso Output Folder 1
crispresso_output_folder_1 (Positional Argument)
Help: First output folder with CRISPResso analysis
Type: str
Crispresso Output Folder 2
crispresso_output_folder_2 (Positional Argument)
Help: Second output folder with CRISPResso analysis
Type: str
Sample 1 Name
-n1, --sample_1_name
Help: Sample 1 name
Sample 2 Name
-n2, --sample_2_name
Help: Sample 2 name
Reported Qvalue Cutoff
--reported_qvalue_cutoff
Help: Q-value cutoff for significance in tests for differential editing. Each base position is tested (for insertions, deletions, substitutions, and all modifications) using Fisher's exact test, followed by Bonferroni correction. The number of bases with significance below this threshold in the quantification window are counted and reported in the output summary.
Type: float
Default: 0.05
Disable Guardrails
--disable_guardrails
Help: Disable guardrail warnings
Type: bool
Default: False
Use Matplotlib
--use_matplotlib
Help: Use matplotlib for plotting instead of plotly/d3 when CRISPRessoPro is installed
Type: bool
Default: False