[mira_talk] Re: Question: padded or unpadded outputs
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 18 Mar 2015 19:59:30 +0000
On Wed, Mar 18, 2015 at 7:44 PM, lenis vasilis <val1@xxxxxxxxxx> wrote:
> Yes, they are very similar, only 3-5 bases are mismatching.
> The problem is that there are some regions with low coverage
> and some others that I have picks with around 50% with one
> letter and around 50% with other. I don't know if this is based
> on assembly- mapping error or a pcr error.
I would try a single assembly of all three lines together, which
should give a consensus.
It may be a real variation in the population, or a sequencing error,
or even as you say a PCR error. But I wouldn't be worrying about
tiny differences like this unless they are in a region of interest
(e.g. within a gene important for your research question).
Alternatively, you could design primers and use "Sanger"
capillary sequencing to check these regions in more detail.
But I would need a strong reason to do all that work.
Peter
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