how can I compare two samples of RNA-seq Generally

Question

[lkianmehr]

Hi

I have a general question. what should I do if I want to compare two samples of RNA-seq generally?

thanks in advance

Leila

Answer 1

[GouthamAtla]

Quantify the gene/transcripts --> normalize (TPM/TMM/FPKM/RPKM) and do a Spearman's correlation.

If you dont have annotations, use stringtie to assemble transcript structures.