bean profile¶

`bean profile`: Profile editing patterns¶

bean profile my_sorting_screen.h5ad -o output_prefix --pam-col '5-nt PAM'`# Prefix for editing profile report`

Output¶

Above command produces prefix_editing_preference.[html,ipynb] as editing preferences (see example).

Full parameters¶

usage: bean profile [-h] [-o OUTPUT_PREFIX] [--replicate-col REPLICATE_COL]
                    [--condition-col CONDITION_COL] [--pam-col PAM_COL]
                    [--control-condition CONTROL_CONDITION] [-w WINDOW_LENGTH]
                    [--save-fig] [--reporter-length REPORTER_LENGTH]
                    [--reporter-right-flank-length REPORTER_RIGHT_FLANK_LENGTH]
                    bdata_path

Positional Arguments¶

bdata_path: Path to the ReporterScreen object to run QC on

Named Arguments¶

-o, --output-prefix

Output prefix of editing pattern report (prefix.html, prefix.ipynb). If not provided, base name of bdata_path is used.

--replicate-col

Column name in bdata.samples that describes replicate ID.

Default: 'replicate'

--condition-col

Column name in bdata.samples that describes experimental condition. (sorting bin, time, etc.)

Default: 'condition'

--pam-col

Column name describing PAM of each gRNA in bdata.guides.

--control-condition

Control condition where editing preference would be profiled at. Pre-filters data where bdata.samples[condition_col] == control_condition.

Default: 'bulk'

-w, --window-length

Window length of editing window of maximal editing efficiency to be identified. This window is used to quantify context specificity within the window.

Default: 6

--save-fig

Save .pdf of the figures included in the report.

Default: False

--reporter-length

Length of reporter sequence in the construct.

Default: 32

--reporter-right-flank-length

Length of the right-flanking nucleotides of protospacer in the reporter.