The OmicsBox’s tool to perform the Clustering of Single-cell RNAseq [http://manual.omicsbox.biobam.com/user-manual/omicsbox-modules/module-transcriptomics/single-cell-data-analysis-tools/single-cell-rnaseq-clustering/] data is based on the widely-used Seurat[4] R package. This analysis groups the cells in clusters with similar gene expression patterns, which should correspond to the same cell type. In addition, this tool performs the filtering [http://manual.omicsbox.biobam.com/user-manual/omicsbox-modules/module-transcriptomics/single-cell-data-analysis-tools/single-cell-rnaseq-clustering/#Single-cellRNAseqClustering-Configuration1and2.Filtering.] and preprocessing [http://manual.omicsbox.biobam.com/user-manual/omicsbox-modules/module-transcriptomics/single-cell-data-analysis-tools/single-cell-rnaseq-clustering/#Single-cellRNAseqClustering-Configuration5and6.DataProcessing.] of the data. So, as in the original paper[2], we filtered the features that are expressed in less than 3 cells and the cells with a minimum total number of detected features greater than 200 and lower than 3000. The normalization method used was Log Normalization and the number of dimensions used during clustering was set to 20. The rest of the parameters were left by default. Moreover, we provide an experimental design to integrate [http://manual.omicsbox.biobam.com/user-manual/omicsbox-modules/module-transcriptomics/single-cell-data-analysis-tools/single-cell-rnaseq-clustering/#Single-cellRNAseqClustering-Configuration3and4.Multi-sampleAnalysis.] the data according to its condition. This would allow cells belonging to the same cell type to cluster together irrespective of whether they come from mutant or wild-type organisms.The Clustering resulted in 14 groups of cells (Figure 6). Each group putatively corresponds to a different cell type, but it is unknown at the moment. Moreover, thanks to the integration step each of the clusters is composed of both wild-type and mutant cells as seen in Figure 7, except cluster 13 which seems to be composed only of wild-type cells.