# Create all files for single-cell best practices.

python ./sc_best_practices_qc.py Nodule_1_3pct_contam ../Nodule_1_gex_only/outs/filtered_feature_bc_matrix.h5 ../Nodule_1_gex_only/outs/raw_feature_bc_matrix.h5 3 > Nodule_1_3pct_contam.out 2> Nodule_1_3pct_contam.err &
python ./sc_best_practices_qc.py Nodule_2_3pct_contam ../Nodule_2_gex_only/outs/filtered_feature_bc_matrix.h5 ../Nodule_2_gex_only/outs/raw_feature_bc_matrix.h5 3 > Nodule_2_3pct_contam.out 2> Nodule_2_3pct_contam.err &
python ./sc_best_practices_normalization.py Nodule_1_3pct_contam
python ./sc_best_practices_normalization.py Nodule_2_3pct_contam
python ./sc_best_practices_feature_selection.py Nodule_1_3pct_contam
python ./sc_best_practices_feature_selection.py Nodule_2_3pct_contam
python ./sc_best_practices_dimensionality_reduction.py Nodule_1_3pct_contam
python ./sc_best_practices_dimensionality_reduction.py Nodule_2_3pct_contam
python ./sc_best_practices_clustering.py Nodule_1_3pct_contam
python ./sc_best_practices_clustering.py Nodule_2_3pct_contam

# Perform dataset integration with Seurat for cellranger and QC Strict datasets

Rscript ./soynod.source.R > soynod.source.err 2>&1 &

# Transform output for cloupe

cd for_cloupe
cat notes.txt | bash