[maq-help] maqview

[Loic B. <lb...@fa...>]

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 the .fq
from solexa. And they quality is > for the whole read. I have seen this
only at the edge of sequence for now though. Do you know where this could
come from and those it mean something for the quality?

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 for
presentation...

Not very fundamental questions as most of it is working fine.

Regards,
Loïc