Contents
What is Seurat object?
The Seurat object is a representation of single-cell expression data for R; each Seurat object revolves around a set of cells and consists of one or more Assay-class objects, or individual representations of expression data (eg. RNA-seq, ATAC-seq, etc).
What does it mean to normalize data?
Data normalization is generally considered the development of clean data. Data normalization is the organization of data to appear similar across all records and fields. It increases the cohesion of entry types leading to cleansing, lead generation, segmentation, and higher quality data.
What is a UMI 10X?
UMI counts represent the absolute number of observed transcripts (per gene, cell or sample). As absolute counts, they are not normalized for sequencing depth, technical variation or RNA content per cell.
What is the difference between barcode and UMI?
UMI is an acronym for Unique Molecular Identifier. UMIs are complex indices added to sequencing libraries before any PCR amplification steps, enabling the accurate bioinformatic identification of PCR duplicates. UMIs are also known as “Molecular Barcodes” or “Random Barcodes”.
What is scRNA-seq used for?
scRNA-Seq provides deeper insight to the multi-tiered complexity of different cells within the same tissue type. scRNA-Seq has now been adapted widely into other methods in the single-cell RNA sequencing field. In this method, single cells are isolated manually under a microscope and lysed.
Is there way to manually define clusters in Seurat and determine?
I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I produce two subsets by the SubsetData function, is there a way to feed them into some other function that would calculate marker genes?
How to find the findallmarkers function in Seurat?
I think you are looking to FindAllMarkers function from Seurat. As you said, you just have to define your ident, that have to have the structure of a table (cell names as names and cluster as value): You can specify several parameters in this function (type of DE to perform, thresholds of expression, etc).
How to define a cluster and find markers?
So I have a single cell experiments and the clustering id not great I have a small groups of 6 cells (I know it is extremely small, but nonetheless I would like to make the most of it) that are clearly isolate in UMAP and display marker that I am interresting in. I managed to get those cells names in barcode (e.g.: AGCCAGCTCGCTTTAT).
Can you use Seurat to cluster cells on tSNE?
Seurat continues to use tSNE as a powerful tool to visualize and explore these datasets. While we no longer advise clustering directly on tSNE components, cells within the graph-based clusters determined above should co-localize on the tSNE plot.