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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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Not m6A knockout sample. #35

Closed litao1503 closed 3 years ago

litao1503 commented 3 years ago

Hi I am new to bioinformatics - I want to be able to identify m6A but am confused by the knockout/knockdown question in xpore-diffmod. In some species, m6A knockdown samples are very difficult to obtain. If we do not m6A knockout sample information, can I continue to use xpore to identify m6a.

Thank you for any guidance on this topic Regards Tao

ploy-np commented 3 years ago

Hi @litao1503, What samples do you have? xPore is a tool to identify differential modifications so it requires at least 2 conditions which are assumably different in modifications. Otherwise, it cannot detect the modification.

litao1503 commented 3 years ago

Hello @ploy-np ， Thanks for the response. Here is the more detailed description: I have four tea plant samples from different growth periods, and I have performed nanopore DRS sequencing on them. I want to compare the m6A modification between four samples. However, all four samples were grown in a natural state, excluding the m6A knockdown samples. I don't know whether it is reliable to use xpore for m6a identification in this case.

ploy-np commented 3 years ago

Hi @litao1503,

Sorry for late reply. Yes, you can compare m6A modification between those samples without m6A knockout/knockdown samples.

litao1503 commented 3 years ago

Thank you so much ploy-np for helping me. Best Regards