scRNASeq analysis Transcript abundance and gene abundance

Question

[SG]

What is the code ,pipeline to get transcript abundance or gene abundance in cell type for scrnaseq data.

Example - If pbmc data has different kinds of cells but I want to get gene abundance or transcript abundance for my gene of interest in monocytes.How can that be done?

Kindly guide.

[Ram]

What have you tried?

[SG]

Thanks for replying.

I am a beginner ,trying to work out a hypothesis. I want to do 2 things- a)Identify dif lymphocyte classes in blood from publicly available scRNA seq data b)See what is the transcript abundance of say gene X in these dif classes of lymphoctes

I don't know how to do the anlaysis.If I have to download the GSM i.e sample barcode,matricx etc files.Or will I need FASTQ or BAM files.

How to proceed?

Answer 1

[jared.andrews07]

How to proceed?

Read OSCA and/or the Seurat vignettes. You can work from the gene counts.

[SG]

Thanks for providing the valuable resources.

When I see the transcript abundance of say gene X in these dif classes of lymphoctes compared to if I use Kallisto or Salmon to get transcript compatibility count, how are these different?

The concept of getting to know which gene transcripts are abundant in a subset of cell(dif classes of lymphocytes) - will we actually call it differential gene expression ? But will it also help us to know gene abundance/transcript abundance of gene of interest?

These 2 things of using kallisto for alignment and mapping to get gene reads vs wanting to know gene abundance in subset of cells.Its quite confusing since in scRNA seq pipeline the Kallisto step to generate count matrix is first,count matrix is nothing but no. of genes that aligned to the reference genome so its transcript quantification/gene abundance while clustering is later.

[rpolicastro]

Read OSCA, it goes over this.

[SG]

Ok will do that.Thanks!