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.
________________________________________
From: Sébastien Boisvert [[email protected]]
Sent: Tuesday, January 07, 2014 11:46 PM
To: Rick White
Cc: [email protected]
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
> <[email protected] <mailto:[email protected]>>
> 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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