[mira_talk] Re: minimum number of reads to join contigs
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 10 Jun 2010 19:09:37 +0200
On Donnerstag 10 Juni 2010 Davide Scaglione wrote:
> Thanks a lot for your detailed and helpful reply!
> Just to double-check..when you talk about chimera detection, are you
> refering to "spoiler detection" -AS:sd??
No. -SK:ascdc. New parameter, not present in current documentation (which I am
reworking right now).
> In this case I think I will do like this; cause I'm using three different
> strain, I will assemble each strain separately with spoiler detection
> switched on.
> Then I will assemble again the resulting contigs together, with spoiler
> detection off...assuming that the contigs are good and real ones...thus
> eligible to join everything they want.
> Is it a good plan?
Don't know, try it out (but -SK:ascdc) and please report back your findings
here, I'd be interested to know what you think of it.
> PS: I swear, as soon as I get a final assembly I will stop to bother you!
Uh oh ... something like a "final" assembly does not exist, especially not
with EST data :-)
B.
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