This tool can be used to setup the Seurat object from two possible inputs:
As inputs, user can give EITHER
a .tar packed folder of 10X Genomics files output files: barcodes.tsv, genes.tsv and matrix.mtx
-NOTE, ONLY these files in a single folder, the tool won't work if you have sub folders in your .tar package!
(the three files are generated by the Cell Ranger -pipeline, and can be found under a folder corresponding to the hg19-folder in this example),
a (DropSeq) digital gene expression (DGE) matrix (which one can generate using Digital expression tool).
Make sure that your input is assigned correctly (under the parameters).
After setting up the object, some basic filtering is performed. At this step, user can define:
Next, some quality control plots are drawn in the QC-plots.pdf file.
Note that it might be easier to view this large pdf with the external viewer.
The first plot shows the number of genes (nGene), UMIs (nUMI) and the percentage of mitochondrial genes (percent.mito) in the cells. The next plot compares the percent.mito and nGene to nUMI. These plots can be used to estimate the outliers: the upper limits for number of genes per cell and mitochondrial percentage. Check the plots and determine these cut-offs, and use them in the filtering & regression tool.
If you have multiple samples, use the "Sample or group name" parameter to name your sample. These names are used later in the tools meant for multiple sample analysis, such as the CCA and integrated analysis tools. Choose short names, like "CTRL", "TREAT".
For more details, please check the Seurat tutorials.