I am confused about what's next when I do a differential expression analysis. I made a DE analysis with one sample, two conditions and no replications (I know that I should have replications, but the experiment was done in that way).
I have the list of transcripts from the DE, but when I open both transcriptomes and look for the transcripts (say TRINITY_DN12605_c0_g1_i1), in the first transcriptome (the one of the first condition), the sequence is longer than the second transcriptome. How should I handle that in order to generate the proteome? I am doing it right? Which sequence to use (the one from the first condition or the second)?
Thanks in advance.