I have digital raw read counts of HTG EdgeSeq Oncology Biomarker Panel (OBP). Whatever I am googling I am not finding anybody used DESeq2 for differenial expresseion in this assay. I have done Differential expression with DESeq2 though. In this assay the expression levels of 2559 genes are assessed. Do you thing I can use DESeq2 for differential expression in this assay?
People in this publication used DESeq2 for HTG assay https://www.htgmolecular.com/assets/htg/publications/2018MyersMicroRNABiomarkersfor_Parkinsons.pdf
Although this is on whole transcriptom HTG on miRNAs rather than targeted sequencing
Thank you for any information