[mira_talk] Re: Getting observed insert size etc for paired end reads
- From: Alan Tsang <alantsangmb@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 14 Feb 2014 15:15:43 +0800
Dear Peter,
How do you interpret the min target size of 22?
What is your read length? Might I know why is the target size smaller than
the read length?
Thanks.
Alan
2014-02-14 10:58 GMT+08:00 Alan Tsang <alantsangmb@xxxxxxxxx>:
> Hello Bastien,
>
> I am using mira 4.0 right now.
> And I am making an assembly setting the template_size = 100 2000
> autorefine and segment_placement = ---> <---
>
> After all, the result maf file just report the template_size same as my
> input manifest file:
> @Version 2 0
> @Program MIRALIB
> @ReadGroup
> @RG name SomeHiseqReadsIGotFromTheLab
> @RG ID 1
> @RG technology Solexa
> @RG strainname Monkey
> @RG templatesize 100 2000
> @RG segmentplacement FR
> @RG segmentnaming solexa
> @EndReadGroup
>
> How can I know the templatesize after refine? Thanks.
>
> Alan
>
>
> 2014-02-13 18:32 GMT+08:00 Bastien Chevreux <bach@xxxxxxxxxxxx>:
>
> > On February 13, 2014 at 10:48 AM Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
>> wrote:
>> > [...]
>> > Those are the predictions for each of the five passes - settling down
>> to a mean
>> > template size of approx 230, standard deviation 114, skew 0.77, min 24,
>> max 480.
>> >
>> > However, the MAF header seems to have the min/max from the first pass
>> (22, 515),
>> > is that an error?
>>
>> Yes. And no, it currently depends a bit on your manifest file.
>>
>> If the segment_placement is not known, MIRA determines the placement in
>> the first pass and the size in the second pass. If you gave the placement
>> (other than "unknown") as parameter in the manifest, then the size is
>> directly determined in the first pass. Though maybe I should change that as
>> first pass assemblies are a bit of a "warm-up" and can include quite some
>> misassemblies. That's more of a problem for large libraries I think, though
>> I need to ponder about this whether I should not push that to second pass
>> per default.
>>
>> Size predictions from subsequent passes however are ignored on purpose
>> as MIRA will have used the previous predictions to place reads and thus
>> have rejected a couple of pairs which fell outside the prediction. If one
>> recalculates predictions on that, the results will be ever shrinking ranges
>> which is not what you want.
>>
>> B.
>>
>>
>
>
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