Base Editor iGUIDE (BEiGUIDE) quantifies base edits in on and off-target cut sites detected by iGUIDE when a base editor-Cas9 fusion enzyme is used.
After running iGUIDE, BEiGUIDE analyzes each position of the protospacer to identify statistically significant changes in the observed nucleotide frequency relative to the expected nucleotide. Please see our pre-print for more details
devtools::install_github('agmcfarland/BEiGUIDE')BEiGUIDE::quantify_edits(
base_directory = "path/to/base_directory",
output_directory = "path/to/output_directory",
analysis_name = "my_analysis",
abundance_cutoff = 5,
end_distance_from_cut_site = 25,
cut_site_start_distance_within_gRNA = 4,
cut_site_start_distance_outside_gRNA = 4,
reference_genome_path = 'path/to/genome.fasta',
editable_base = 'A',
expected_edit = 'G',
binomial_p_value_threshold = 0.05,
binomial_direction = 'greater',
n_processors = 6,
overwrite = FALSE
)
BEiGUIDE::quantify_edits_analysus(
quantify_edits_output_path = '/path/to/quantify_edits/output'
)| Parameter | Type | Description | Default |
|---|---|---|---|
| base_directory | Character | Base directory where input data is located | REQUIRED |
| output_directory | Character | Directory where output data will be saved | REQUIRED |
| analysis_name | Character | Name of the analysis | "quantify_edits" |
| abundance_cutoff | Numeric | Minimum read count for including an edit site | 3 |
| expected_cut_distance_from_pam | Numeric | Distance from PAM where the cut site is expected | 3 |
| end_distance_from_cut_site | Numeric | Maximum distance from the cut site to consider bases | 20 |
| cut_site_start_distance_within_gRNA | Numeric | Distance within the gRNA to start considering cut sites | 3 |
| cut_site_start_distance_outside_gRNA | Numeric | Distance outside the gRNA to start considering cut sites | 3 |
| reference_genome_path | Character | Path to a FASTA file used to retrieve reference genome sequence | REQUIRED |
| editable_base | Character | Original base targeted for editing | 'A' |
| expected_edit | Character | Base that the editable base is expected to be converted into | 'G' |
| binomial_p_value_threshold | Numeric | P-value threshold for binomial test of significance | 0.05 |
| binomial_direction | Character | Direction of binomial test ('greater', 'less', 'two.sided') | 'greater' |
| n_processors | Numeric | Number of CPU cores to use for parallel processing | 4 |
| overwrite | Logical | Whether to overwrite existing analysis output | TRUE |
- Wrapper to run from command line
- Docker image