I have 3 samples of RNAseq in 3 different conditions (no replicates). This is Illumina MiSeq 2x150bp reads. No reference genome available.
First, I've performed quality filtering with trimmomatic, de novo assembly with Trans-Abyss (k-mer size = 96), then I've mapped reads onto contigs with BWA. I have also performed clustering transcripts by Corset. Now I would like to perform differentiation analysis and GO analysis.
So my questions are:
- How to perform differentiation analysis for data with no replicates? Which tool would you recommend?
- What tool for GO analysis?
Thank you in advance,