How could I analyse the differential expression of a particular gene with RNA-seq data?

Question

[bioAddict]

Hi everyone! I'm new in RNA-seq data analysis. I'm interested in the differential analysis of a set of particular genes from an open access raw data. So I want to know which tools I need to use, specially after the mapping. So please help me I'm confuse.

[seidel]

Read the edgeR Userguide. It's a good discussion of many of the issues involved, has discussions of experimental designs, a section on gene set testing, and is very accessible.

Answer 1

[swbarnes2]

Use RSEM to count genes, then use DESeq2 or EdgeR. Of course, you have to process the whole dataset, not just your favorite subset.