Examples -------- The following is an example of an BASH file to run the ST pipeline. This example is for version 1.3.3 of the ST pipeline. .. code-block:: bash #!/bin/bash # FASTQ reads FW=/YOUR_RUN/R1.fastq.gz RV=/YOUR_RUN/R2.fastq.gz # References for mapping, annotation and nonRNA-filtering MAP=/mouse/GRCm38_86v2/StarIndex ANN=/mouse/GRCm38_86v2/annotation/annotation.gtf CONT=/mouse/GRCm38_86v2/ncRNA/StarIndex # Barcodes settings ID=/stpipeline/ids/YOUR_IDs.txt # Output folder and experiment name # Do not use / or \ in the experiment name OUTPUT=/your_experiment_folder EXP=YOUR_EXP_NAME # Running the pipeline st_pipeline_run.py \ --output-folder $OUTPUT \ --ids $ID \ --ref-map $MAP \ --ref-annotation $ANN \ --expName $EXP \ --htseq-no-ambiguous \ --verbose \ --log-file $OUTPUT/${EXP}_log.txt \ --contaminant-index $CONT \ $FW $RV