[mira_talk] Re: minimum number of reads to join contigs
- From: "Davide Scaglione" <gianza@xxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 17 Jun 2010 12:21:52 +0200
Of course on the last version Bastien linked on the bord (3.1.15) it's working.
By the way keep in mind that there is a misunderstandig.
ascdc is a -CL parameter. try as first to use -CL:asdcd
And please let me know what's your opinion, I'm using it too for EST. Do you?
davide
From: bio5yz
Sent: Thursday, June 17, 2010 1:33 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: minimum number of reads to join contigs
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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