[mira_talk] Re: EST SNP

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 30 Sep 2009 23:26:06 +0200

On Mittwoch 30 September 2009 Miguel Pinheiro wrote:
> [...]
> For example: the read F2F5W1J01DTYAP belongs to the strain "xpto" and in
> the first step it appears in the "step1_out.caf".
> In the second step it appears in the "remain" and doesn't appear in the
> "xpto_out.caf" file. Why???

Hello Miguel,

I suppose it has been sorted out as singlet in step 2. This can happen, though 
I'd need to search for the exact circumstances.

> Another possible enhancement that could be done is the ability to analyze
> more than 8 strains at a time. In my case I have 7 strains and the "remain"
> strain. So, with this pipeline it is not possible to use more than 8
> strains simultaneously.

I don't remember exactly why I capped the number of strain in MIRA to 8 ... I 
think some data structure had only 3 bits remaining and could not imagine that 
people would like to assemble more than 4 or 5 strains.

I've put that suggestion onto the feature request list, but it will not appear 
anytime soon I'm afraid.

> Where do I get a table with the description of TAGs that appear in the caf
> files??

Does the section "Tags used in the assembly by MIRA and EdIt" of the main 
manual answer your question? :-)

Regards,
  Bastien


-- 
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts: