RNA Seq analysis - DESEQ2 no significative p-value/log2(FC)

[Pandore]

I’m supposed to analyze datas obtained from a RNA-seq, but my DESEQ2 results doesn’t make any sense. I don’t have any significative p-value for 62000 genes.

I dont think it’s normal because im replacting an experience that has a lot of differential results.

cutadapt (remove adapters and quality control)
RNA Star with reference genome hg38
Featurecount for quantification
Deseq2 for differential analysis

I also tried with Salmon but it’s the same thing.

[igor]

Hi @Pandore
62k genes is a big number for genes. It seems you work with transcripts or extended set of genes. Tools such as DESeq2 apply a correction for multiple testing, and correction correlates with number of genes.
The samples do not separate on PCA plot according to factors (group), in in this situation absence of DEGs is not surprising. Check MDS plot section in this tutorial for explanation of PCA/MDS plots

Galaxy Training: 2: RNA-seq counts to genes

Kind regards,
Igor