how to get the site-level labels of the arabidopsis

[hanyishui0612]

Thank you for your outstanding work!

I'd like to ask you how to get the site-level labels of the arabidopsis.Looking forward to your reply.

[yuukiiwa]

Hi @hanyishui0612,

Here is the method section on obtaining the labels for Arabidopsis:

To determine whether a site is modified or not, we included the labels provided by Parker et al.54 and statistically significant sites obtained from running xPore diffmod on all four replicates of the VIRc and vir-1 mutants with pooling option and a minimum read threshold of 20. Additionally, we also performed multiple test corrections using Benjamini–Hochberg procedure and set an alpha rate of 0.05 for both methods and only consider a site to be modified according to either one of the methods if it passes this threshold.

Thanks!

Best wishes,
Yuk Kei

[hanyishui0612]

Hi @hanyishui0612,

Here is the method section on obtaining the labels for Arabidopsis:

To determine whether a site is modified or not, we included the labels provided by Parker et al.54 and statistically significant sites obtained from running xPore diffmod on all four replicates of the VIRc and vir-1 mutants with pooling option and a minimum read threshold of 20. Additionally, we also performed multiple test corrections using Benjamini–Hochberg procedure and set an alpha rate of 0.05 for both methods and only consider a site to be modified according to either one of the methods if it passes this threshold.

Thanks!

Best wishes, Yuk Kei

Thank you for your reply!I want to know how to get the labels provided by Parker.Can you tell me?And is there any script code for related operations?

[hanyishui0612]

Hi @hanyishui0612,

Here is the method section on obtaining the labels for Arabidopsis:

To determine whether a site is modified or not, we included the labels provided by Parker et al.54 and statistically significant sites obtained from running xPore diffmod on all four replicates of the VIRc and vir-1 mutants with pooling option and a minimum read threshold of 20. Additionally, we also performed multiple test corrections using Benjamini–Hochberg procedure and set an alpha rate of 0.05 for both methods and only consider a site to be modified according to either one of the methods if it passes this threshold.

Thanks!

Best wishes, Yuk Kei

hi,I want to train a Arabidopsis thaliana model.Now I get the nanopolish eventalign result.By reading the help documentation, I want to run m6anet dataprep again and add other columns based on the obtained data.info.Then train this data.lables.info file.I have questions about labels. I got the results of xpore diffmod (VIRc and vir1). The parts that passed the verification are the modified sites. How to find unmodified sites? Looking forward to your reply