The problem I have isn't really a bioinformatic problem but I came across a hard nut to crack when analyzing my RNA-seq results. I had 3 conditions in triplicate: - 1 = control - 2= expressing 2 isoforms of a protein - 3= expressing 1 isoform of the protein
Seq generated 50 million 75 bp single end reads per sample.
The DE analysis I realized using cuffdiff gave me the following results: - 1 vs. 2 = 400 DEG - 1 vs. 3 = 50 DEG - 2 vs. 3 = 800 DEG
The same .BAM files analyzed using DESeq2 gave me more "marked" results: - 1 vs. 2 = 700 - 1 vs. 3 = 10 DEG - 2 vs. 3 = 2300 DEG
Here both analyzes show negligible DEG between condition 1 and 3. I know that DE analysis has the purpose to highlight significantly deregulated genes but to have so much DEG between 1 vs 2 and 2 vs 3 means there is something going on in my third condition right ? even tho there is not much DEG between control and third condition ? I don't know how to put this results into words.
Does anyone has encountered a similar situation ?
Thanks for the help you can provide !