Hi Biostars, 

I got two output files (*genes.results and *isoforms.results) from aligning reads to the Trinity denovo assembly(Trinity.fasta) with Bowtie2 and expected read counts with RSEM. Out of two output files, which one should I feed to DESeq2 for identifying DEGs. 

Any suggestions will be appreciated. Thanks in advance. 
That means if I want gene level LFC I need to input *genes.results and for transcript level LFC *isoforms.results file should be used. Thank you.