scRNAbox - aces/cbrain GitHub Wiki
scRNAbox is a single-cell RNA sequencing (scRNAseq) pipeline specifically designed for analyzing data under a High-Performance Computing (HPC) systems using the Slurm Workload Manager. The scRNAbox pipeline leverages the Seurat v4 framework and incorporates eight analytical steps into a comprehensive scRNAseq analysis that provides the foundation for further investigations.
More information can be found on the scRNAbox tool page.
For this example, we used the tutorial available on the scRNAbox page. It illustrates the steps taken to analyze the midbrain dataset (Smajic et al. 2022) that was presented in their pre-print manuscript. This dataset describes single-nuclei transcriptomes from the post-mortem midbrains of five individuals with Parkinson’s disease (PD) and six controls sequenced separately.
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To create your project and upload your files, please follow steps 1 and 2 from Cellranger Count available in the previous section.
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For more information about downloading the midbrain dataset, please visit their documentation.
File requirement: file(s) has to be registered as a FASTQ collection and follow the FASTQ file naming convention.
From the Files tab, select the required file(s) and click launch.
From the tool box, select the tool, execution server and the version then Launch scRNAbox count
If you want to run a quick run test, we recommend selecting Converter-1 or Converter-2.
- Choose the data provider where you want to save your results (for example MainStore)
- Choose your project
- Set up your Task parameters
Notes:
- For this exercise, we will go through steps 1-2
- The task parameters values follow the scRNAbox github page tutorial
- Every option marked with a red asterisk is mandatory
- Step 1
- Step 2
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Click on Tasks to monitor the status of your task(s)
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Once your task is completed (or failed), you will get a new notification
- Click on the task to get the results
- Click on the Output files to view your results
You can go deeper into the files by clicking on Expand
