[mira_talk] Re: K-mer coverage filtering
- From: Chenling <chenlingantelope@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 22 Aug 2014 15:24:25 -0700
I have several datasets, the lowest one is a about 200, and the highest 2000.
Chenling
On Aug 22, 2014, at 3:22 PM, Adrian Pelin <apelin20@xxxxxxxxx> wrote:
> What is the nucleotide coverage of your organism of interest?
>
> Sincerely,
> Adrian
>
>> On Aug 22, 2014, at 6:20 PM, Chenling <chenlingantelope@xxxxxxxxx> wrote:
>>
>> That could work too but for now all my work is done on a laptop…
>>
>>> On Aug 22, 2014, at 3:17 PM, Adrian Pelin <apelin20@xxxxxxxxx> wrote:
>>>
>>> Why not just denovo assemble everything, then blast your contigs vs
>>> endosimbionts?
>>>
>>> Sincerely,
>>> Adrian
>>>
>>>> On Aug 22, 2014, at 5:03 PM, Chenling <chenlingantelope@xxxxxxxxx> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I have been trying to assemble endocellular symbiont genomes from
>>>> sequencing of both the host and the symbiont. So far I have been pooling
>>>> out reads from the symbiont by mapping them to a closely related strain
>>>> and getting the reads that map for the assembly. I was just made aware of
>>>> an extra step that might significantly improve this method. Basically I
>>>> would calculate the k-mer coverage for the mapped reads, and because my
>>>> symbiont has much higher coverage than the host (about 10 times higher),
>>>> once I have the expected coverage I would then filter all my reads by the
>>>> k-mer coverage criteria. So this would allow me to get reads even if they
>>>> are divergent from my reference sequence.
>>>>
>>>> Is there a way to work this in Mira?
>>>>
>>>> Thank you!
>>>> Chenling
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>>>
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>>
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