question about the modification category

[huawen-poppy]

Hello! Thanks for your powerful tool!

I have a question about the detected site, is there any way to know that the modification type? Let's say we have several NNGNN kmers, then can we know whether the modification is 7-methylguanylate or 2-methylguanylate? For all the NNANN kmers, are they all the m6A modification?

[yuukiiwa]

Hi @huawen-poppy,

xpore only outputs sites that are differentially modified in two groups samples (pairwise comparison), so if one of your sample is enriched with 7-methylguanylate or 2-methylguanylate or m6A and another sample is unmodified, then you will be able to tell the specific type of modification the site is.

Thanks!

Best wishes,
Yuk Kei

[huawen-poppy]

Hi @yuukiiwa Thank you very much for your response! I have two conditions: control and treatment. Each condition has 3 replicates. I don't have any unmodified samples. In this case, I still get some results from xpore. I would like to know do the unmodified samples necessary to make the results reliable?
Besides, I don't have much background in RNA modification. From the result, I can know it is the middle site of the kmer get modified. Does NNANN only mean for the m6A modification (maybe there are other kind of modification on the A but not called m6A modification)? NNCNN corresponding to the m5C modification? NNGNN is either 7-methylguanylate or 2-methylguanylate? What is the modification type of NNTNN?
Thank you very much for your time!