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The run of the script will override the original output of the pipeline.

Steps for RNA-seq pipeline:

1. Save backup of the report folder of the analysis: 4_reports,
   cp -r 4_reports 4_reports.bak
2. Navigate into the folder of the R script:
   cd 4_reports/report_output_XXXXXXXX_XXXXXX 
3. Change the report.Rmd script.
4. Run the command:
   PATH=$PATH:/home/labs/bioservices/services/miniconda2/envs/utap/bin
   /home/labs/bioservices/services/miniconda2/envs/utap/bin/Rscript -e "rmarkdown::render('report.Rmd')" --verbose
5. The output file is: 4_reports/report_output_XXXXXXXX_XXXXXX/report.html

Steps for MARS-seq pipeline:

1. Save backup of the report folder of the analysis: 10_reports,
   cp -r 10_reports 10_reports.bak
2. Navigate into the FIRST folder of the R script (of the analysis without counts correction):
   cd 10_reports/report_output_XXXXXXXX_XXXXXX 
3. Change the report.Rmd script.
4. Run the command:

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