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Editing ABIF (Read 4578 times)

Jan 17^th, 2011 at 9:44am

Poh Offline
YaBB Newbies

Posts: 46

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 | )

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Reply #1 - Jan 17^th, 2011 at 5:51pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

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.

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Reply #2 - Jan 18^th, 2011 at 7:58am

Poh Offline
YaBB Newbies

Posts: 46

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.

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Reply #3 - Jan 18^th, 2011 at 7:37pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Thanks for suggestion! We will keep that in mind.

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