Re: [maq-help] maqview

[Heng Li <lh...@gm...>]

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=

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