Re: [maq-help] maqview
Status: Beta
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From: Heng Li <lh...@gm...> - 2007-10-05 14:49:35
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Hello Loic, Thank you for the feedback. It is good to know you are using it. I =20 have a bit worried that requiring OpenGL may bring troubles to end =20 users. As for your questions, we have realized that displaying the reference=20 +consensus, which is currently missing, is definitely useful to =20 endusers. Our next move is to add both reference and consensus =20 sequences in the maqview. This functionality will appear in maqview's =20= next release. (other questions are answered below) On 5 Oct 2007, at 15:26, Loic Baerlocher wrote: > Hello, > > maqview is a great improvement, thank you for the job. They are a few > points i need your wisdom with. > > Some reads are shown as lowercase although they are uppercase in =20 > the .fq > from solexa. And they quality is > for the whole read. I have seen =20 > this > only at the edge of sequence for now though. Do you know where this =20= > could > come from and those it mean something for the quality? I think this is probably because we are using different cut-off to =20 show upper/lower bases. ">" means Q=3D29 and in maqview the cut off, I =20= guess, is 30. Yes, we should improve this. > Also is there a way to display the ambiguity code for the consensus > sequence? I have it the cns.fq but the display is always A/T/G/C. > > I have tried the reference display but i only get a text output. Did i > miss something? > > Last, can i start counting from 1 instead of zero on the consensus > sequence in maqview display? It doesn't bother me but it isn't good =20= > for > presentation... Yes, we should show 1-based coordinates. We will change that. There are also several missing functionalities in maqview, such as =20 selecting reference, showing paired end reads, displaying reference =20 and consensus and so on. We, actually mainly Jue who wrote maqview, =20 will implement these gradually. Many thanks, Heng > > Not very fundamental questions as most of it is working fine. > > Regards, > Lo=EFc > > ----------------------------------------------------------------------=20= > --- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a =20 > browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > maq-help mailing list > maq...@li... > https://lists.sourceforge.net/lists/listinfo/maq-help |