I do DGE analysis (sample A vs sample B) using Salmon then Tximport (without scaling) then DEseq2. Everything works fine but my problem is that sample A is contaminated with red blood cells so that half of the total read counts map on globin transcripts. So TPM/counts values in sample A and FC values (A vs B) are artificially lowered.
My question : can I manually remove the contaminating transcripts (less than 10 transcripts, easy to identify) from the TXI output file before loading into DESeq2? If doing so, should I use scaledTPM values?
Thank you for your help.