[mira_talk] Re: K-mer coverage filtering
- From: Adrian Pelin <apelin20@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 22 Aug 2014 18:22:17 -0400
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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