questions about default NDR values if running in de novo mode

[alexyfyf]

Hi @cying111

I would like to test the de novo mode with bambu, when I run Bambu 3.11 (although the log still says 3.9)

se <- bambu(reads = bam.files, 
             stranded = F, 
             genome = fa.file, ncore = 32
            )

I notice I can leave NDR as default (NULL value I assume), but it still gives an output. I read the documentation, and did not find how the default NDR was set in de novo mode, nor it prints out the NDR caculated automatically as in the guided mode. Even in the generated se object, I did not find a field that I can extract the NDR value (I have tried to look into the metadata(se)).

Could you explain a bit more and suggest how to use the de novo mode correctly? I have tested with some values, such as setting NDR = 1, but it gave too many novel transcripts (I assume it just set everything as novel and output it?).

Thanks a lot.

Alex

[cying111]

Hi Alex,

Thank you for reaching out. In de novo mode, if NDR is not specified, a default threshold of 0.5 is applied. You can check this value in the NDR column of the rowData in the SE object. Setting NDR = 1 will report all novel transcripts identified from the reads. But you can perform filtering based on the NDR column based on your preference.

Hope this helps clarify your questions!
Thank you and feel free to reach out if you have further questions!

Warm regards,
Ying