bean qc

bean qc: QC of reporter screen data

bean qc \
  my_sorting_screen.h5ad             `# Input ReporterScreen .h5ad file path` \
  -o my_sorting_screen_masked.h5ad   `# Output ReporterScreen .h5ad file path` \
  -r qc_report_my_sorting_screen     `# Prefix for QC report` \
  --control-condition presort        `# "condition" column in the control sample before selection. Mean gRNA editing rates in these samples are reported. ` \
# Inspect the output qc_report_my_sorting_screen.html to tweak QC threshold

bean qc \
  my_sorting_screen.h5ad              \
  -o my_sorting_screen_masked.h5ad    \
  -r qc_report_my_sorting_screen      \
  --control-condition presort         \
  #[--count-correlation-thres 0.7 ...]\
  -b   # Removes the failing replicates without enough number of good quality samples.

bean qc supports following quality control and masks samples with low quality. Specifically:

• Plots guide coverage and the uniformity of coverage

• Guide count correlation between samples

• Log fold change correlation when positive controls are provided

• Plots editing rate distribution

• Identify samples with low guide coverage/guide count correlation/editing rate and mask the sample in bdata.samples.mask

• Identify outlier guides to filter out

Output

Above command produces

• my_sorting_screen_masked.h5ad without problematic replicate and guides and with sample masks, and

• qc_report_my_sorting_screen.[html,ipynb] as QC report.

Full parameters

usage: bean qc [-h] [--count-correlation-thres COUNT_CORRELATION_THRES]
               [--edit-rate-thres EDIT_RATE_THRES] [--lfc-thres LFC_THRES]
               [-o OUT_SCREEN_PATH] [-r OUT_REPORT_PREFIX] [-b] [-i]
               [--no-editing] [--dont-recalculate-edits] [--tiling TILING]
               [--replicate-col REPLICATE_COL]
               [--sample-covariates SAMPLE_COVARIATES]
               [--condition-col CONDITION_COL]
               [--target-pos-col TARGET_POS_COL] [--rel-pos-is-reporter]
               [--edit-start-pos EDIT_START_POS] [--edit-end-pos EDIT_END_POS]
               [--posctrl-col POSCTRL_COL] [--posctrl-val POSCTRL_VAL]
               [--lfc-conds LFC_CONDS] [--control-condition CONTROL_CONDITION]
               [--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, --out-screen-path

Path where quality-filtered ReporterScreen object to be written to

-r, --out-report-prefix

Output prefix of qc report (prefix.html, prefix.ipynb)

--reporter-length

Length of reporter sequence in the construct.

--reporter-right-flank-length

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

QC thresholds

--count-correlation-thres

Correlation threshold to mask out.

Default: 0.7

--edit-rate-thres

Mean editing rate threshold per sample to mask out.

Default: 0.1

--lfc-thres

Positive guides’ correlation threshold to filter out.

Default: -0.1

Run options

-b, --remove-bad-replicates

Remove replicates with at least two of its samples meet the QC threshold.

Default: False

-i, --ignore-missing-samples

If the flag is not provided, if the ReporterScreen object does not contain all condiitons for each replicate, make fake empty samples. If the flag is provided, don’t add dummy samples.

Default: False

--no-editing

Ignore QC about editing. Can be used for QC of other editing modalities.

Default: False

--dont-recalculate-edits

When ReporterScreen.layers[‘edit_count’] exists, do not recalculate the edit counts from ReporterScreen.uns[‘allele_count’].

Default: False

Input .h5ad formatting

--tiling

Specify that the guide library is tiling library without ‘n guides per target’ design

--replicate-col

Label of column in bdata.samples that describes replicate ID.

Default: 'replicate'

--sample-covariates

Comma-separated list of column names in bdata.samples that describes non-selective experimental condition. (drug treatment, etc.)

--condition-col

Label of column in bdata.samples that describes experimental condition. (sorting bin, time, etc.)

Default: 'condition'

--target-pos-col

Target position column in bdata.guides specifying target edit position in reporter

Default: 'target_pos'

--rel-pos-is-reporter

Specifies whether edit_start_pos and edit_end_pos are relative to reporter position. If False, those are relative to spacer position.

Default: False

--edit-start-pos

Edit start position to quantify editing rate on, 0-based inclusive.

Default: 2

--edit-end-pos

Edit end position to quantify editing rate on, 0-based exclusive.

Default: 7

--posctrl-col

Column name in ReporterScreen.guides DataFrame that specifies guide category. To use all gRNAs, feed empty string ‘’.

Default: 'target_group'

--posctrl-val

Value in ReporterScreen.guides[posctrl_col] that specifies guide will be used as the positive control in calculating log fold change.

Default: 'PosCtrl'

--lfc-conds

Values in of column in ReporterScreen.samples[condition_label] for LFC will be calculated between, delimited by comma

Default: 'top,bot'

--control-condition

Values in of column in ReporterScreen.samples[condition_label] for guide-level editing rate to be calculated

Default: 'bulk'