Does Tombo plot kmer for RNA use reverse complement kmers?

[patbohn]

Hi,

I want to plot kmer values of direct RNA sequenced samples, and got it to work successfully, but it appears that C and U center bases have the lowest signal, while A and G center nucleotides have the highest signal. This is pretty much the exact opposite of the graphics shown here https://nanoporetech.github.io/tombo/plotting.html#k-mer-signal-levels so I am not quite sure what could be going on here. Do you have an idea?

Edit: Attached an example 3-mer plot

IVT_RNA_curlcake_3mer.kmer_distribution.pdf

[marcus1487]

The plot kmer function should be plotting the signal levels on forward kmers. I have not looked at a kmer table or summary for direct RNA data, but this does indeed sound a bit odd. I'm not quite sure what could be going on here.