[mira_talk] Re: Presenting PCR data as paired end reads?
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 28 Jun 2010 21:10:17 +0100
On Mon, Jun 28, 2010 at 6:15 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Montag 28 Juni 2010 Peter wrote:
>> [...]
>> However, suppose we don't do the Sanger sequencing. What if we have
>> just the fact that a pair of PCR primers amplified a region of about
>> (say) 1000bp? This could be presented as a paired end read (the
>> forward and reverse primer sequences of say 20bp each). Do you think
>> it would be useful to try and present this information to MIRA or are
>> such "reads" just too small?
>
> I'd say "too small". Though 20bp is around the lowest overlap I'd recommend
> using, so you might give it a try. Might work, might not. But it will fail
> miserably if the gap you are trying to close is repetitive.
OK.
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?
Thanks,
Peter
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