Deg Difference in Deseq2

Question

[j.k.owaresat]

I ran Deseq2 tool on 6 RNA of Aedes mosquitoes (7dpi) where 3 rna sequences are infected with Dengu and 3 rna sequences are in control conditions. Here I got only 9 degs (up+down). Is the deg output number is wrong? Here, I ran Trimmomatic. Then, the alignment rates for all 06 sequences in HiSat2 tool were 90-91%. The raw Count % for all 06 sequences in Featurecount tools were 60-64%. After that the little number of deg result is correct? Or, If the deg number is wrong what can be the reasons behind that? I am waiting for all of your kind suggestions.

[ATpoint]

Or, If the deg number is wrong what can be the reasons behind that?

• Truely no differences
• noise and variation
• underpowerment
• wrong code
• preprocessing issues
• basically anything (cannot tell because you show neither code, plots or anthing). [[ Please read before posting a question ::: How To Ask A Good Question ]]

Answer 1

[swbarnes2]

If the code ran at all, you probably did it correctly. Since you have such a simple design, you probably set up the design correctly.

If your read counts are not extraordinarily low, the input data is probably fine, though 90% seems a little low for alignment, and 60% seems a little low for gene assignment. But none of that means your data is wrong, just that the quality was a little lacking.

If you can show a bit of info to confirm all this, the simplest explanation is that the tissue you tested (whole mosquito?) doesn't show much change when infected with virus. I would think if you were sick, and we put your whole body in a blender and did RNAseq, we might not find much either, unless a major organ was literally dying. And the mosquitos are clearly healthy enough to fly around, so it might make sense that there is little to no detectable effect.

Did you include the dengue genes in your gene count? Can you detect the infection directly?