This tutorial describes how to run alternative differential expression (DE) methods on LUHMES CROP-seq data. All file paths here are relative to this working directory: /project2/xinhe/yifan/Factor_analysis/LUHMES/
.
Location: run_deseq.R
;
Command line usage example:
Rscript run_deseq.R --out_folder=processed_data/DESeq2/dev_top6k_negctrl/ --marker=ADNP --NTC_only=TRUE --permute=FALSE
marker
: the gRNA perturbation condition to test the differential effects,
NTC_only
: whether to compare with only nontargeting control cells or all cells in other conditions.
Edit the Python script submit_DE_jobs_in_batches.py
, which can submit sbatch jobs for all gRNA targets.
Make sure to modify the sbatch script defined in make_DEG_sbatch()
and loop over all conditions.
To submit jobs, run the edited script: ./submit_DE_jobs_in_batches.py
.
Each gRNA condition vs negative control: processed_data/DESeq2/dev_top6k_negctrl/
;
Each gRNA condition vs the rest of cells: processed_data/DESeq2/dev_top6k/
;
Location: run_MASTcpmDetRate.R
;
Command line usage example:
Rscript run_MASTcpmDetRate.R --out_folder=processed_data/MAST/dev_top6k_negctrl/ --marker=ADNP --NTC_only=TRUE --permute=FALSE
marker
: the gRNA perturbation condition to test the differential effects,
NTC_only
: whether to compare with only nontargeting control cells or all cells in other conditions.
Edit the Python script submit_DE_jobs_in_batches.py
, which can submit sbatch jobs for all gRNA targets.
Make sure to modify the sbatch script defined in make_DEG_sbatch()
and loop over all conditions.
To submit jobs, run the edited script: ./submit_DE_jobs_in_batches.py
.
Each gRNA condition vs negative control: processed_data/MAST/dev_top6k_negctrl/
;
Each gRNA condition vs the rest of cells: processed_data/MAST/dev_top6k/
;
Location: scmageck/run_scmageck.R
;
Command line usage example (works on all gRNA conditions at once):
Rscript scmageck/run_scmageck.R --permute=FALSE
Each gRNA condition vs negative control: scmageck/scmageck_lr.LUHMES.dev_res_top_6k.rds
.