Using xpore vs m6Anet

[baibhav-bioinfo]

Hello,
i have plant (RNA004) data of two conditions with 3 replicates for each.
i want to predict the m6A modified sites in each replicate then do a differential modification analysis between conditions.

Out of m6Anet and Xpore which one is more suitable?
can i use m6Anet to predict and then use some test manually to find Diff modified sites?

[yuukiiwa]

Hi @baibhav-bioinfo,

The m6anet RNA004 model was trained using human data, still, you can test that out on your plant samples.

Still, xpore would be our software fo differential modifications analysis between conditions. Here is the RNA004 kmer model that you will have to supply in the config.yml file when running xpore diffmod:

https://github.com/GoekeLab/xpore/blob/RNA004_kmer_model/xpore/diffmod/RNA004_5mer_model.txt

Thanks!

Best wishes,
Yuk Kei

[baibhav-bioinfo]

Thanks @yuukiiwa for the response, we will try with Xpore.