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visualize user graph data (Read 6478 times)
Jun 9th, 2011 at 1:24am

elizabeth   Offline
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Hi all,

I'm impressed with the program! One thing that I would like to do is display quantitative annotation data. By this I mean plot along the sequence numerical values that correspond to a base or a range of bases. (like the GC plot you already have implemented, but with user data...)
This would be useful for all sorts of things, in my case I'm interested in plotting methylation data.

File formats i know of that support this include the .wig (wiggle) format
http: // genome.ucsc.edu / goldenPath / help / wiggle.html
and the .bed format
http: // genome.ucsc.edu / goldenPath / help / bedgraph.html

Do you know if any of the file formats that are already supported could be used to load this type of quantitative annotation?

Otherwise, I suggest a feature to modify the "import annotation from CSV" dialog box so that in the "select role for column" dialog you could choose an option like "value"

so that you could load a file like
#position value
110 0.875000
116 1.000000
161 0.500000
162 0.941176
311 0.358974
501 0.153846
512 0.333333

which is the simplest form of .wig file, just associating a value to a nucleotide position.

Thanks!!!

Elizabeth
 
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Reply #1 - Jun 10th, 2011 at 1:15pm

Konstantin Okonechnikov   Offline
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Hi Elizabeth,

Currently quantative annotation data is supported only for DNA chromatogram files (ABI and SCF formats), but unfortuantely this functionality can not be reused to visualize BED or WIG.

I've created the issue based on your request in the bug-tracker:
https://ugene.unipro.ru/tracker/browse/UGENE-408

Regarding the "Import from CSV" function: the WIG file can be parsed with simple script. However, I've found out that scripting doesn't work properly.

Another issue has been created:
https://ugene.unipro.ru/tracker/browse/UGENE-405

The issues are planned to be resolved in version 1.9.4 (to be realeased in July) however it will be possible to test them from weekly snapshot once they are accomplished. You can register in the bug-tracker and subscribe to the issues ("watch" them) in order to recieve updates about the development status.

Best regards,
Konstantin, UGENE team
 
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Reply #2 - Jun 10th, 2011 at 5:27pm

elizabeth   Offline
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Hi Konstantin,

   Thanks for your response, I'll be watching the bug-tracker and looking forward to the next version!

Regards,

Elizabeth
 
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Reply #3 - Sep 20th, 2011 at 6:53pm

Loddi   Offline
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Hi, I would also be very interested in such a feature. - push
 
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