rania-o

Hello, thanks for your fast answer. It's an RNA sequence of 443 bp that contains A, C, G and U. The reads contain also A, C, G and U. Rania

I just discovered that the sam file from minimap2 has replaced Us with Ts. Is it necessary for nanopolish to have a match between the alignment file and the reference...

Hi @jts I converted the Us to Ts in the reference sequence and it works. You were right, Nanopolish doesn't tolerate Us in the reference, especially that minimap2 too converts...

No, I didn't. I just used other tools.

Hi @enovoa, Thank you for your reply. I still don't understand which method I have to rely on as I've got only few positions in common between the two methods....

Hi @enovoa, Thanks a lot for these specifications. I already used demo data and other public data to test tools, and yes we do have a control sample (IVT), but...

Aaah, yes I see what you mean. Indeed, we already have this type of control (oligo with two known modified positions), but unfortunately with all the tools I have tested,...

Yes, I understand your position, it is difficult to have constant parameters or methods for all analyses, since these will depend rather on the data types. Thank you for your...

@keenhl Drummer, Epinano, Eligos, Xpore ...