[mira_talk] Re: minimum number of reads to join contigs
- From: bio5yz <bio5yz@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 16 Jun 2010 17:33:36 -0600
Hi Bastien,
My data is also experiencing assembly issues due to possible chimera
sequences. Trying '-SK:ascdc' as a parameter though my MIRA3.0.5 install
does not seem to recognize the flag.
* Parameter section: '-SK'
* unrecognised string or unexpected character: ascdc
Which version is this function available?
Thanks,
Michael.
On Thu, Jun 10, 2010 at 11:09 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
> 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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