I have performed the abundance estimation using RSEM which outputted the genes.results and isoforms.results. I would like to import the isoforms results into DESeq2 pipeline. I followed the tximport pipleine for RSEM like following but when I checked the rownames, it gave me gene names instead of transcript names
rsem.files=list.files(".","*.isoforms.result") txi.rsem=tximport(rsem.files, type = "rsem",txOut = T)
Could anyone please guide what mistake I committed.
Thanks in advance.