On 08/01/14 03:06 AM, Hornung, Bastian wrote:
> You might laugh, but I've found in at least one case that providing mean/stdv
> actually makes the result worse (don't ask me why...).
> I've before been a bit hesitant not to do so, because I doubted the accuracy
> of a possible estimation, but I later got PacBio reads and mapped my data to
> them, and there seems to be virtually no difference between the estimation
> and the actual insert size.
Sometimes, when seeds are too short, it is barely possible to estimate the
length of mate pair library that are longer than 10kb.
> ________________________________________
> From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca]
> Sent: Tuesday, January 07, 2014 11:46 PM
> To: Rick White
> Cc: denovoassembler-users@lists.sourceforge.net
> Subject: Re: [Denovoassembler-users] Ray Assembly with Mate Pairs?
>
> On 07/01/14 05:41 PM, Rick White wrote:
>> Hello,
>>
>> I do. I have a standard fragment library + a long mate pair library.
>>
>> How would I make use of them in Ray? What would my options/command be?
>>
>
> mpiexec -n 99 Ray -k 31 \
> -p standard_1.fastq.gz standard_2.fastq.gz \
> -p mate_1.fastq.gz mate_2.fastq.gz 20000 2000 \
>
>
> (You can also try without the manually provided mean and standard deviation
> ("20000 2000").)
>
>> Cheers
>> Rick
>>
>>
>> On Tue, Jan 7, 2014 at 2:38 PM, Sébastien Boisvert
>> <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>>
>> wrote:
>>
>> On 07/01/14 05:01 PM, Rick White wrote:
>>
>>
>> Hello,
>>
>> Is there a way to assembly long 20kb mate pair libraries on Ray?
>>
>>
>> You'll need shorter libraries to complement the 20kb mate pair library.
>>
>>
>> Both used the MiSeq 250x2 bp technology.
>>
>> Cheers
>> Rick
>>
>>
>>
>>
>
>
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