[mira_talk] Re: minimum number of reads to join contigs
- From: bio5yz <bio5yz@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 18 Jun 2010 11:09:53 -0600
Thanks for the correction! I have a 400k 454 EST dataset that has been
giving me issues using other assemblers and look like it may contain chimera
sequences between key locations. Will see how this function works.
Cheers,
Michael.
On Thu, Jun 17, 2010 at 4:21 AM, Davide Scaglione <gianza@xxxxxxxxxx> wrote:
> 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 <bio5yz@xxxxxxxxxxxxxx>
> *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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>
>
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