[mira_talk] Re: Question: padded or unpadded outputs
- From: lenis vasilis <val1@xxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 18 Mar 2015 19:44:03 +0000
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.
On Mar 18, 2015, at 7:28 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
> On Wed, Mar 18, 2015 at 7:12 PM, lenis vasilis <val1@xxxxxxxxxx> wrote:
>> Hi,
>>
>> Thank you very much for your support.
>> I did the conversion by using the maf2sam.py, the script that you have in
>> your blog.
>
> OK, that should work too - I updated it to cover the current MIRA
> file format.
>
>> Now, at the moment I'm trying to identify how the unpadded file
>> filled the gaps from the padded one.
>
> Browsing the assembly in Tablet/IGV should help give you
> a feel for the inserts and how padded versus unpadded
> output from MIRA is a different representation of the same
> assembly.
>
>> I used Mira three times with the data of three different lanes.
>> The three unpadded consensus are different in 3-5 bases only.
>> If the assembly was alright I suppose that these three consensus
>> should be exactly the same, shouldn't be?
>
> No. If you are very very lucky, then maybe. Even assuming
> the DNA that went into the three lanes was the same, you will
> have different errors in the reads, so there is no guarantee
> the three assemblies will give you identical contigs. I would
> expect the ending points of the contigs to differ slightly,
> and in lower coverage regions apparent SNPs between
> the three assemblies seem quite likely.
>
> But at a high level, the three assemblies should be very similar.
>
> Peter
>
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