Hi, I'm new to DESeq2 so I apologise if my question is a bit naive. my dataset consists of 3 biological replicates of Control and treatment and I have performed Ribosome profiling and RNA Seq. I have a counts matrix which looks like this: Con1 Con2 Con3 treatment1 treatment2 treatment3 transcript1 0 1 1 2 1 1 transcript2 1 1 2 3 4 4 transcrpt n 2 3 3 0 1 0

where the counts are ratios of TPM counts: RiboSeq/RNASeq that come from transcriptome mapping. I ran the DESeq2 but got padj=1 which indicates that I'm probably using the wrong input? Should I give my count data in a different format?

Thanks in advance for any suggestions

Katerina

Check out our RNA-seq workflow, or the vignette. Both indicate that DESeq2 should have counts as input.