fursham-h/factR

Predicting NMD function

Closed this issue · 3 comments

Drosofriends commented

Hi, I'm using your tool for my analysis, when I use the function "predict NMD" I obtain the table with transcript, stop_to_lastEJ, num_of_downEJs, 3'UTR_length and is_NMD.
For my analysis I want to determine the specific PTC position in my novel isoforms.
Is it possible to implement another column in the output with the PTC position? Can I obtain this information from the custom_GTF and NMD_object?
Thanks for the help.

fursham-h commented

Hi @Drosofriends. Thanks for using factR! That's actually a good point, I can add a new column with potential PTC coordinates together with the output of predictNMD. I'll work on it soon and update you.

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fursham-h commented

Hi @Drosofriends. My apologies for taking this long, but we have made modifications to predictNMD() to output PTC coordinates as a separate column. Do test this out on your data and provide feedback on it :)

fursham-h commented

Closing this issue for now.