[mira_talk] Re: Negative insert size (feature request)
- From: Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>
- To: Bastien Chevreux <mira_talk@xxxxxxxxxxxxx>
- Date: Sun, 14 Aug 2011 20:50:16 +0200
> On Aug 14, 2011, at 18:34 , Nestor Zaburannyi wrote:
>> I have one Paired-end solexa file in which sequences /1 and /2 are expected
>> to overlap by approx. 50 bases. I tried to use "fastq-join" (
>> http://code.google.com/p/ea-utils/wiki/FastqJoin ), but i am not satisfied
>> with results. Can MIRA handle "negative" inserts sizes? I think it will
>> perform much better than standalone tools. Just a thought.
> MIRA oes not work with "insert sizes" per se, but with "template insert
> sizes". It stems from the old Sanger sequencing days when pieces of DNA
> (templates) were inserted into sequencing vectors to be sequenced.
> As such, the "template insert size" does not define the distance which
> separates two reads, but the expected size of a DNA template and therefore
> the distance which separates the outer ends of two reads. As result to this,
> the size cannot get below zero.
Got it.
> For what you want to do, MIRA will be perfectly happy if you set the minimum
> size to 0.
Not quite understood. Why 0? If my reads are 2 x 120 and they overlap by 50
bases, then the average insert should be 2 x 120 - 50 = 190 bp. With 0.3
deviation it should be, for example:
-GE:tismin=130:tismax=250
MIRA will do what i want?
Sincerely yours
Nestor
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