Sorting screen tutorial without reporter edits¶

Screens without editing outcome, where each gRNA is assigned to a target.

Library design	Each guide RNA (or other perturbation such as ORF) has a specified target.
Selection	Cells are sorted based on FACS signal quantiles

Here, we consider an example where BEAN uses the external count without reporter, gRNA and sample information to infer the per-target effect sizes.

Example workflow¶

screen_id=var_mini_screen_noedit
working_dir=tests/data/

# 1. Given that we have gRNA count for each sample, generate ReporterScreen (.h5ad) object for downstream analysis.
bean create-screen ${working_dir}/gRNA_info.csv ${working_dir}/sample_list.csv ${working_dir}/var_mini_counts.csv -o ${working_dir}/${screen_id}

# 2. QC samples & guides
bean qc \
  ${working_dir}/${screen_id}.h5ad             `# Input ReporterScreen .h5ad file path` \
  -o ${working_dir}/${screen_id}_masked.h5ad   `# Output ReporterScreen .h5ad file path` \
  -r ${working_dir}/qc_report_${screen_id}     `# Prefix for QC report` \
  -b                                           ` # Remove replicates with no good samples.

# 3. Quantify variant effect
bean run sorting variant \
    ${working_dir}/${screen_id}_masked.h5ad \
    -o ${working_dir}/ \
    --uniform-edit --ignore-bcmatch            `# As we have no edit/reporter information.` \
    [--fit-negctrl [--negctrl-col target_group --negctrl-col-value NegCtrl]]                                      `# If you have the negative control gRNAs.`

Input file spec¶

gRNA_info.csv: Should have name, target columns. You can also specify target_group column whose value indicate PosCtrl/NegCtrl for control gRNAs.
sample_list.csv: Same requirement for the full run. See examples for ``sorting` screens <https://github.com/pinellolab/crispr-bean/blob/main/tests/data/var_mini_samples.csv>`_ and ``survival` screens <https://github.com/pinellolab/crispr-bean/blob/main/tests/data/sample_list_survival.csv>`_.

See the example input files here.

See Subcommands for the full details.