biocorecrg/master_of_pores

#QUESTION: to detect m6A RNA modifications

hqs10 opened this issue · 3 comments

hqs10 commented

Dear all, Dear @lucacozzuto,

I am happy to inform that sample comparison Tombo model worked perfectly on our data set.

However, we also need to use tombo detect_modifications alternative_model with the --alternate-bases 5mC 6mA option.
Please let me know, do you have any "nanomod.nf" available, which is set on these model and params?

How can we limit nonamod to search for modifications among specific motifs (e.g. DRACH motifs)?

Really appreciate any reply.

Stan

ADelgadoT commented

Hi Stan,

Currently NanoMod can not be limited to specific kmers. However, if you want to add these modifications, you can submit a pull request and we'd be happy to incorporate these changes.

Thank you,

Anna

hqs10 commented

Hi Stan,

Currently NanoMod can not be limited to specific kmers. However, if you want to add these modifications, you can submit a pull request and we'd be happy to incorporate these changes.

Thank you,

Anna

Thanks for the reply, Anna!

Sure. If we are successful in modifying NanoMod to search for specific kmers, we would be happy to submit the pull-request.

Please let me also know, did you try the following tombo method
tombo detect_modifications alternative_model with the --alternate-bases 5mC 6mA?

Best regards,

Stan

ADelgadoT commented

Hi Stan,

Sorry for the late reply. We have not used the tombo detect_modifications alternative_model with the --alternate-bases 5mC 6mA inside MoP. However, NanoMod could be modified to run Tombo in this mode. If you are successful, we would be happy to submit the pull-request.

Thanks!

Anna