Good morning,
My task is to perform a Differential Expression Analysis on 31 tissues of an individual to see variation among gene expression. I'm not interesting in all genes expressed but actually I have to focus my analysis only on 2 particular genes. I trimmed my raw reads and check the quality, I mapped the reads with HISAT2, I assembled my reads with StringTie and I generated two CSV files containing the count matrices for genes and transcripts with the prepDE.py script following this pipeline (https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual). As I just said now I have to perform DEA for 2 genes on my 31 different tissues.
How can I proceed? Could you suggest me a pipeline to follow possibly using DESeq2?
Thank you in advance for your time and suggestion!
