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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> Editing ABIF https://forum.ugene.net/forum/YaBB.pl?num=1295232252 Message started by Poh on Jan 17^th, 2011 at 9:44am

Title: Editing ABIF
Post by Poh on Jan 17^th, 2011 at 9:44am

Hi!

I am testing ABI editing in ugene. I found that there is no function for me to delete a miscalled base. While I could assign any of the 4 bases, I could not remove a miscall "N". How could I remove the miscall using ugene?

temp.PNG (146 KB | )

Title: Re: Editing ABIF
Post by Konstantin Okonechnikov on Jan 17^th, 2011 at 5:51pm

Currently it's not possible to delete the bases from chromotgram editor - writing for ABI format is not supported.
However you can always delete a part of sequence (context menu, edit sequence -> remove subsequence) "explicitly"

We'll put this feature on our TODO-list, hope it will be included in next release.

Title: Re: Editing ABIF
Post by Poh on Jan 18^th, 2011 at 7:58am

Removing subsequence is not intuitive to end users.

I would suggest opening up a new fasta, and let the user curate the result by deleting/changing bases that is incorrect, then export the fasta. Miscalled bases could contribute to mistranslation and what looks like mutation while it is not.

Maybe it would be better to basecall the ABI as accurate as possible first, by using tools like tracetuner http://sourceforge.net/projects/tracetuner/

So that we could minimize manual correction of the base called.

Title: Re: Editing ABIF
Post by Konstantin Okonechnikov on Jan 18^th, 2011 at 7:37pm

Thanks for suggestion! We will keep that in mind.