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 ?