Run the following code for the Quick Start in the docker DeepSeqDock - bicbioeng/DeepSeqDock GitHub Wiki

For the default (QT), Run this code:

• python scripts/build_myHarmonizer_fromDataset.py -d supporting/train.csv -v supporting/valid.csv -m supporting/meta.csv

For the other preprocessing steps ("LS" "RLE" "VST" "TMM" “none”), Run this code:

• python scripts/build_myHarmonizer_fromDataset.py --d supporting/train.csv -v supporting/valid.csv -m supporting/meta.csv -o <output_file_name> -p <preprocessing_steps>

For the other preprocessing steps ("GeVST" "GeTMM” "TPM" - which needs genelength.csv file), Run this code:

• python scripts/build_myHarmonizer_fromDataset.py --d supporting/train.csv -v supporting/valid.csv -m supporting/meta.csv -o <output_file_name> -g supporting/genelength.csv -p <preprocessing_steps>