B_ALL_genome_wide_crispr

Count Data

Broad PoolQ count data for the primary screen are located in these directories:

• 200406
• 200627
• RH_resequenced_counts_files

Broad PoolQ count data for the validation screen are located in these directories:

• crispr_041822_validationScreen/fromBroad

Primary screen

data were imported and organized using the script:

• mageck/mageckPrimary_Screen.Rmd

Pool/Sample assembled count matricies are in mageck directory:

The files are:

• invitro.pool[ABCDEF].txt
• invivo.pool[ABCDEF].txt

mageck (version 0.5.9.4) test was run on Linux system with these scripts:

• mageck/mageck_invitro_pool[ABCDEF].sh
• mageck/mageck_invivo_pool[ABCDEF].sh

all associated mageck output for these runs are included in the mageck folder

Validation screen

Broad PoolQ count data for the validation screen are located in this directory:

• crispr_041822_validationScreen/fromBroad

data were imported and organized using the script:

• crispr_041822_validationScreen/mageck/mageckFlute_RamosValidationScreen.html

mageck (version 0.5.9.4) test was run on Linux system with this script:

• crispr_041822_validationScreen/mageck/mageck_sr.sh

mageck output for this run is included in the mageck folder