Can Xpore detect RNA modification other than m6A?

[fulaibaowang]

Hi,

i am wondering how good is xpore detect other RNA modification like ψ and ADP-ribosylation or is it mainly designed for m6A/RNA methylation?

Thanks in advance!

Yun

[yuukiiwa]

Hi Yun (@fulaibaowang),

xpore is a tool for detecting differential modification, so one would have to compare an m6A-writer knockout to a WT to detect the presence of m6A. If you know the conditions of your samples, where a modification is enriched, then you will expect xpore to show the sites with the modification as differentially modified.

Thanks!

Best wishes, Yuk Kei

[fulaibaowang]

Hi YuK,

thanks! I was just wondering if you have tested the performance of xpore on detecting low abundance of modification. m6A is relative abundant but there is other modification that could have lower abundance with which might have problem with false positve calls.

[g-s-2018]

Hi YuK, I am trying to detect the positions within the RNA where nucleoside analogs are incorporated. Since their incorporation is random, I don't have the exact locations. Based on the charge of the nucleotide located in the middle position of the RNA sequence, is it possible to identify modified nucleosides? I am using in vitro transcribed RNA as a control for comparison. Additionally, in this case, how can I interpret the sign of the modification rate? I am not looking for gain or loss. Can I just consider the negative sign ad the test < control which means the position is modified. Thanks in advance