How to filter highly transcribed genes?

Question

[Parham]

Hi,

I am wondering how can I make a list of highly transcribed genes from my RNA-seq data? What package to use and what values to consider (FPKM, read counts, etc)?

The idea is to make a list of highly transcribed genes from my control experiment and then see how many or which one of the DEGs in my treatment experiment are among the highly transcribed genes.

Any help is appreciated. Let me know if you need more info.

Answer 1

[GouthamAtla]

Use htseq-count to get the read counts per gene/exon. Get the normalised counts from edgeR and sort them. You need to have a count matrix to use edgeR.

If you do not have replicates or different conditions, try simple FPKM normalisation.

[Parham]

Thanks Geek_y. Since I am familiar with DESeq2 package, I guess it is the same to use normalized counts created by DESeq2, do you know about that?

[GouthamAtla]

It should be.

[Parham]

Then I'm wondering that if I have one set of control experiment and two or more different sets of experiments, the list of highly transcribed genes can vary since they are normalized to the experiment and then filtered? Is it correct to think like that?