bean create-screen

bean create-screen: Create ReporterScreen object from flat files

bean create-screen gRNA_library.csv sample_list.csv gRNA_counts_table.csv

Input

  • gRNA_library.csv (variant screen example, tiling screen example)

  • sample_list.csv (sorting screen example, variant screen example)

  • gRNA_counts_table.csv: Table with gRNA ID in the first column and sample IDs as the column names (first row) gRNA_library.csv and sample_list.csv should be formatted as Input file format. (example)

Full parameters

bean-create-screen parameters

usage: bean create-screen [-h] [-e EDITS] [-b X_BCMATCH] [-o OUTPUT_PREFIX]
                          gRNA_info_table_csv samples_info_table_csv
                          gRNA_counts_table_csv

Positional Arguments

gRNA_info_table_csv

Path to gRNA info .csv table, with index at first column and column names at the first row.

samples_info_table_csv

Path to sample info .csv table, with index at first column and column names at the first row.

gRNA_counts_table_csv

Path to gRNA counts .csv table, with index at first column and column names at the first row.

Named Arguments

-e, --edits

Path to edit counts .csv table, with index at first column and column names at the first row.

-b, --X-bcmatch

Path to barcode-matched count .csv table, with index at first column and column names at the first row.

-o, --output-prefix

Output file prefix (output will be saved as output_prefix.h5ad). If not provided, gRNA_counts_table_csv file prefix is used.