I am applying
salmon quant with
--geneMap option to quantify RNA-SEQ to gene level count files. I plan to proceed with DE using Deseq2.
Is it OK to use
tximport as follows:
tximport(files, type="salmon", countsFromAbundance="no", txIn=T , txOut=T ).
In other words, apply the gene count files as if these are transcripts and avoid any upper level aggregation. I did not find the natural way of applying gene counts to