pseudouridine (Ψ) modifications in RNA

[gaoxiangcao]

Hi, I’m using modkit pileup to analyze pseudouridine (Ψ) modifications in RNA. However, when I visualize the results in IGV, I see that many called modification sites are not located on T bases. Is this expected behavior, or does it indicate a high false positive rate in the model?

[ArtRand]

Hello @gaoxiangcao,

What is likely happening is there are single base mismatches (V>U) and these have pseU calls on them. You can omit thes bedMethyl records by using --motif T 0, then you will only get bedMethyl records that are reference T (/U) positions.