CRISPResso2 Annotation
Download all files 0_Functions.R 1_AnnotateCRISPResso.R, 2_runannovar.sh, and 3_Annotation_render.Rmd and the script to run it all CRISPR_Annotate.sh
Script to run the full pipeline. Change the .sh to executable before running
usage: CRISPR_Annotate.sh [-h]
arguments:
--help show this help message and exit
--input/-i INPUTPATH [input_params] Path to directory containing all Alleles_Frequency_Table.zip files
--gene/-g Gene [input_params] Gene of Interest to grab coordinates (works only with 1 at a time)
--start/-s Start [input_params] Start site
--end/-e Start [input_params] End site
--PAM/-p Pam [input_params] PAM site
--allele/-e Pam Allale [input_params] PAM allele
--output/-o Output [input_params] Output
Example
chmod +x CRISPR_Annotate.sh
./CRISPR_Annotate.sh -p /scratch/nousome/ccbr1046/Annotate_B1B2repeat/ -g BRCA2