List of scripts to run cellranger, report and Tony's code
Examples of most current scripts can be found in /fsx/home/abdalla/perturb_TKT00129
convertSheet.R: converts the guide reference to cellranger format prepCR.R: prepares the files needed to run cellranger files: Per sample csv file in directory csvLibraries runAll.bash: contains cellranger command to run cellranger for all GEX+guide samples runAll2.bash: contains cellranger command to run cellranger for all GEX only samples
crispr_QC.Rmd: is to create the reports to excecute runRMD.bash
runRMD.bash takes in the following parameters Names of samples to run: The molecule sample and the equivalant DMSO sample Directury: GEX+guide cellranger output Same as samples to run but the GEX only files Directury: GEX only cellranger output Name of html file output
Example: runRMD.bash "MOL-00000458-003_NONE_LV00053-01_8_24","DMSO_NONE_LV00053-01_8_24" "/fsx/home/abdalla/perturb_TKT00129/guide_CR/" "MOL-00000458-003_NONE_NONE_0_24","DMSO_NONE_NONE_0_24" "/fsx/home/abdalla/perturb_TKT00129/gex_CR/" "MOL-00000458-003_NONE_LV00053-01_8_24.html"
full exectution example /fsx/home/abdalla/perturb_TKT00129/runReports.bash
Running Tony's code 3 scripts JOB-BATCH.R: Executes the script and takes in the parameters perturbSeqLibMAINv12.R: Runs the code and generates plots perturbSeqBATCHv12: Contains the functions for perturbSeqLibMAINv12.R
Example on how to run Rscript JOB-BATCH.R MOL-00010082-005_COT M082 /fsx/home/abdalla/preturb_RSQ000007_EXP000075/guide_CR/MOL-00010082-005_COT-00000001-003_LV00018-01_Higher/outs/filtered_feature_bc_matrix.h5 /fsx/home/abdalla/preturb_RSQ000007_EXP000075/guide_CR/DMSO_COT-00000001-003_LV00018-01_Higher/outs/filtered_feature_bc_matrix.h5 /fsx/home/abdalla/preturb_RSQ000007_EXP000075/gex_CR/DMSO_COT-00000001-003_NONE_Higher/outs/filtered_feature_bc_matrix.h5 /fsx/home/abdalla/preturb_RSQ000007_EXP000075/RSQ000007_EXP000075_LV00019_crispr_sgrna.csv