[mira_talk] Re: Presenting PCR data as paired end reads?
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 1 Jul 2010 10:28:13 +0100
On Mon, Jun 28, 2010 at 9:13 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Montag 28 Juni 2010 Peter wrote:
>> What if we had sequenced both ends of the PCR fragment? e.g.
>> Two end reads of length 400bp with an estimated fragment length
>> of 1000bp - does that make sense to give to MIRA as a Sanger
>> paired end read?
>
> Yes, very much so. This is, in fact, almost a prototype definition of a paired
> end :-)
>
> Bastien
Do you have any specific recommendations for what to do when
you have more than two reads for a PCR product?
e.g. If I have frag.f1, frag.f2 and frag.r1 (two forward reads from one
end, one reverse read from the other end)? I'm currently treating this
as a single pair, and putting the spare read in as a non-paired read.
What if we did some primer walking, so we have multiple overlapping
reads at both ends of the fragment? Manually pre-merge these and
give them to MIRA as a pair of long composite reads?
I will of course try a few things and see how I get on, but it is nice
to know what others have found works.
Thanks,
Peter
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