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How to show a quality graph for .ABI files? (Read 11707 times)
Jun 30th, 2009 at 2:39pm

mats   Offline
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I'm sure that can viewed a quality graph for .abi files, but i try right now and don't find  such option....maybe i'am confused and i  viewed a quality graph in another software, but i think that was using UGENE software...  Huh

look like this
...
 
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Reply #1 - Jul 6th, 2009 at 10:43am

Alexey Varlamov   Offline
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Ugene displays quality values slightly differently, as bars above  chromatogram peaks. Since version 1.4.1, the bars can be turned on/off via context menu, as displayed on the attached screenshot.
« Last Edit: Jul 6th, 2009 at 2:30pm by Alexey Varlamov »  

qual.png (47 KB | )
qual.png
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Reply #2 - Jul 8th, 2009 at 12:45pm

mats   Offline
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yep, I know about quality bars, but i thought that Ugene could show the graphic too...I am confused, i don't know where saw that type of plot, what software was......but well, thanks for the answer, and , about the topic, is very useful can see a quality graphic, because is more easy find the zones at extremes of the sequences, the limit where the sequence is becoming a good one,  and cut-out the rest for posterior analysis

Oh, what about the colours of quality bars, some equivalence of a phred score, a reference value?
 
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Reply #3 - Jul 9th, 2009 at 8:42pm

Mikhail Fursov   Offline
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The color scheme of quality bars is rather simple: green - low signal, yellow is medium, red - strong signal. The gradient has linear scale and has no equivalence with phred.

I think we can add the functionality you need the UGENE too. Could you describe the method used to build the line chart on your picture in details?
 

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UGENE team
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Reply #4 - Jul 16th, 2009 at 12:14pm

mats   Offline
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This quality graph are displayed for  a service of dna sequencing that I use usually (macrogen).
the red  and the green line are phred score, 16 and 20, respectively.
I don't know nothing about the method of building, sorry.

And thanks for the answers and for the software , Ugene is a very pleasing piece of software, was a very nice surprise for me and my linux system, congrats.  Smiley
 
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