Reference seq. on MAQviewer

[yasutake]

I am using maq 0.6.8 and maqview 0.2.4.

Reference sequence on maqview gets to XXXXX when I opened .map file with o option on the maqview window.

Any idea ?

OS: Opensuse 11.0 x86_64

Thank you.

[acnoll]

Just to start with the simple... did you index the .cns file at the same time as indexing your .map file? If so did you specify the .cns file when running maqview?

[lh3]

Have you tried:

maqindex -c consensus.cns
maqview -c consensus.cns aln.map

Note that the consensus file also contains the full reference sequence.

[yasutake]

Thank you.

My explanation wasn't enough.

I did as follows

1. maqindex -i -c consensus.cns
2. maqview -c consensus.cns sample1.map
<maqview is opend>
3. (Ctrl and +) on the screen of maqview to see the results of 2 samples at once.
4. typed o on the screen of maqview.
5. typed (sample2.map) to open the result of sample2.
<Regarding the sample2, reference seqence is not displayed.>

Dr. Ih3, If you are Dr. Heng Li, could you fix this problem ?

[lh3]

Well, you have to ask Jue, the developer of maqview. I can only answer simple questions. I never use Ctrl+ in fact.

[Aengus]

Hi

I did post a solution to your problem on the maq-help list on 02-12-2008

http://sourceforge.net/mailarchive/forum.php?forum_name=maq-help

There is a problem with maqindex in 0.2.4 and you need to recompile it with a new version of cns_cache.c


Aengus

[dvh]

Note also the issue with maqview and incorrect display of reads with small indels, and Heng Li's response re samtools - see the maq help list.
david