[mira_talk] Re: Assembly finishing
- From: Jan Paces <hpaces@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 14 Apr 2009 15:53:22 +0200
Hi,
Lionel Guy wrote:
> - Is there a way to display the IUPc, UNSc, SRMc, WRMc, etc. tags in
> consed? I have tried, but not succeeded so far
add
<code>
consed.fileOfTagTypes: /usr/local/genome/lib/mira_tags.conf
</code>
into your .consedrc
file /usr/local/genome/lib/mira_tags.conf should look like this:
<code>
SRMr OrangeRed both yes
WRMr Orange both yes
SRMc OrangeRed both yes
WRMc Orange both yes
ORMB orange1 both yes
SROr DarkTurquoise both yes
SROc DarkTurquoise both yes
SAOr SeaGreen both yes
SAOc SeaGreen both yes
SIOr PaleGreen both yes
SIOc PaleGreen both yes
ED_I pink both yes
ED_D pink both yes
ED_C pink both yes
Q454 yellow both yes
STRM lightblue both yes
PSHP orange1 both yes
</code>
> - Is there any alternative to consed (or to gap4, that is not really
> suitable if you have half a million reads)?
I am using consed. Maybe you can look on AMOS, particularly on HAWKEYE
(http://amos.sourceforge.net/hawkeye). If you find something better, let
me know, I did not succeeded.
Jan
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