RNASeq DE analysis between tumor and normal tissues

Question

[debitboro]

Hi all,

I need a helps from you. I have RNASeq data sequenced using Illumina, I want to get the list of DE genes between tumor tissue and the matched normal tissue of 22 individuals, so in total I have 44 samples (22 tumor data vs 22 normal data). What is the recommended way to do the DE analysis of these data ?

What I already tried:

for each sample: Mapping with Tophat2 ===> HTSeq-count for summarization ===> gene-count file (with two columns: gene and sample_name)

so at the end of this step, I have 44 gene-count files

then I used DESeq2 to normalize the data (applied to all the gene-count files, all the gene-count files are merged)

is this a correct way ?

[EVR]

As far I could see, all steps are correct. Just to check, try to find diff expressed genes using some other method(edgeR) just to confirm whether you are getting similar results between DeSeq2 and edgeR.

[debitboro]

thank you Tom, I'll try this