scRNASeq analysis Transcript abundance and gene abundance
1
0
Entering edit mode
12 days ago
swanti ▴ 10

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.

abundance quantification scrnaseq transcript • 375 views
ADD COMMENT
0
Entering edit mode

What have you tried?

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode
12 days ago

How to proceed?

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

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Read OSCA, it goes over this.

ADD REPLY
0
Entering edit mode

Ok will do that.Thanks!

ADD REPLY

Login before adding your answer.

Traffic: 2912 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6