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.

#!/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