What is the recommended approach for quantifying expression of group of genes in specific type of cells?

Question

[obuhovadarina]

I want to analyze how a group of genes sharing the same function is expressed in a certain type of cells. I have downloaded 370 gene sequences of genes with needed function (Fasta format files) from a public database. I am planning to download cellular RNA-seq data as well. I would like to quantify expression of these 370 genes in a transcriptome of these cells. What is the recommended workflow for this type of task?

Looking forward to your replies!

Answer 1

[jared.andrews07]

I would probably just generate normalized counts for all genes in the RNA-seq data via kallisto or salmon and DESeq2 or edgeR, then pull out the genes of interest for comparison/visualization/further analysis.

[obuhovadarina]

Thank you so much! And a last one, how do you pull out the genes of interest for comparison and visualization?

[jared.andrews07]

They will just be in an R dataframe. If you aren't familiar with R, some reading will teach you all about them, including how to slice and subset them.