two replicates intra condition gives no significant results

[glopatriello]

Hi there!

I am performing rmats analysis on RNAseq data of two conditions whose each group have two replicates. The analysis gives no significant results. All events are reported with FDR score equal to 1. I was wondering if these results is biologically true or is strongly dependent on the number of intra-group replicates.

Best regards, Giulia

[EricKutschera]

rmats does not require a minimum number of replicates for each group. Having only two replicates in each group doesn't prevent rmats from reporting significant events. It could be that there is some other issue with your data that leads to all the events having FDR of 1. Maybe the read counts are very low, or the reads are actually very similar between the two groups