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Question about Geneious: Viewing multiple raw chromatograms
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Jul 29th 2010
Hi,
I am considering purchasing Geneious, but I just wanted to know if it were possible to view raw chromatograms in the contig view. I have activated the Chromatogram viewer from the preferences, which allows viewing of the raw chromatogram data for individual Contig assembly fragments. When in contig view, however, Geneious normalises the distance between each base call. Is it possible to view the raw chromatograms in this view, similar to Sequencher and Consed. While this is less "pretty", I think it provides more thorough information on base calls, allowing better identification of incorrect calls.
Cheers.
I am considering purchasing Geneious, but I just wanted to know if it were possible to view raw chromatograms in the contig view. I have activated the Chromatogram viewer from the preferences, which allows viewing of the raw chromatogram data for individual Contig assembly fragments. When in contig view, however, Geneious normalises the distance between each base call. Is it possible to view the raw chromatograms in this view, similar to Sequencher and Consed. While this is less "pretty", I think it provides more thorough information on base calls, allowing better identification of incorrect calls.
Cheers.
Jul 29th 2010
The contig view is essentially and alignment so you can't have the raw uneven spaced chromatogram on it and have it still be an alignment. To view the raw chromatograms you need to go back to the source sequence documents and there should be a link next to the name of each sequence in the chromatogram which will jump you back to the source document which will have the raw trace view available. You can't edit the calls in the raw view but it will give you additional information in making your judgements.
Shane
Shane
Jul 29th 2010
Thanks Shane,
Are there any plans to implement a non-normalised "alignment", such as those in Sequencher and Consed? I think the Consed implementation is particularly elegant. My current workflow for analysing contigs is to inspect an alignment of the multiple chromatograms, looking at the raw trace files simultaneously. Using Geneious would mean I'd have to look at each trace file individually, and then remember what was ambiguous for when I inspected the alignment view. This is a bit clunky. I appreciate that you could skip back and forth through the multiple windows, but this is not ideal, and could easily get confusing. In addition, clicking that link shows the raw trace, but doesn't link to the region of DNA being inspected.
I'm open to suggestions for more efficient ways to analyse my sequenced DNA, but this has always seemed best to me.
Are there any plans to implement a non-normalised "alignment", such as those in Sequencher and Consed? I think the Consed implementation is particularly elegant. My current workflow for analysing contigs is to inspect an alignment of the multiple chromatograms, looking at the raw trace files simultaneously. Using Geneious would mean I'd have to look at each trace file individually, and then remember what was ambiguous for when I inspected the alignment view. This is a bit clunky. I appreciate that you could skip back and forth through the multiple windows, but this is not ideal, and could easily get confusing. In addition, clicking that link shows the raw trace, but doesn't link to the region of DNA being inspected.
I'm open to suggestions for more efficient ways to analyse my sequenced DNA, but this has always seemed best to me.
Jul 29th 2010
You can't really do a non-normalised alignment if the character spacing isn't fixed although I would be interested in seeing screenshots of what you get from Sequencher or Consed since we don't have access to those programs ourselves (send them to shane@biomatters.com).
For the most part, having the traces above the sequences, even normalised, is better because you can compare multiple sequences and see how the base calls stack up. You can always pop out the original sequence file into a separate window which is more like what Sequencher does when viewing chromatograms when I last used it anyway but as you say it can get confusing if there are multiple windows. Best to send us screenshots of what you're after because just talking about this doesn't really get us there and past experience shows it takes much longer to understand what a picture can show instantly.
Shane
For the most part, having the traces above the sequences, even normalised, is better because you can compare multiple sequences and see how the base calls stack up. You can always pop out the original sequence file into a separate window which is more like what Sequencher does when viewing chromatograms when I last used it anyway but as you say it can get confusing if there are multiple windows. Best to send us screenshots of what you're after because just talking about this doesn't really get us there and past experience shows it takes much longer to understand what a picture can show instantly.
Shane
7 days ago
Sorry, forgot that I was halfway through this conversation!
Yes, I agree that having the sequences "in-line" with the alignment is the best. I've sent you an email showing you how Sequencher and Consed achieve this with non-normalised alignments. (I don't think Sequencher has had its UI updated since the '80s!) Basically, they only align one selected base, and scroll the chromatograms accordingly. Clicking a different base scrolls all chromatograms to this new position.
Yes, I agree that having the sequences "in-line" with the alignment is the best. I've sent you an email showing you how Sequencher and Consed achieve this with non-normalised alignments. (I don't think Sequencher has had its UI updated since the '80s!) Basically, they only align one selected base, and scroll the chromatograms accordingly. Clicking a different base scrolls all chromatograms to this new position.
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