[mira_talk] Re: Question: padded or unpadded outputs
- From: lenis vasilis <val1@xxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 18 Mar 2015 20:10:18 +0000
The problem is that I have 9 lanes. To try a single assembly with all these
data was my first thought but I dont believe that I have the amount of ram to
do that.
Each try consumes 65 - 85 G.
As it seems for a job like that I will need more than 0.5 T which I can afford
at the moment.
Thank you very much for the process that you propose me (Sanger), its great to
learn new things and techniques, but I don't believe that I could do something
like that even I wanted to
On Mar 18, 2015, at 7:59 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
wrote:
> 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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