On 02/11/11 05:23 PM, CJ wrote:
> Hi Seb,
>
>    

Hi CJ,

> I have another question about the automatic detection of Distance&  SD
> in the PE reads. I have two Libraries (500bp and 2K),


For the 500 bp, Ray is quite good at it.

For the 2K, Ray should be fine also.

>   but in the
> LibraryStatistics.txt file each Lib shows an AverageOuterDistance ~1K
> with SD ~800.

Did you provide each library ?

like

mpiexec -n 64 Ray -k 31 -p 500bp_1.fastq 500bp_2.fastq -p 2K_1.fastq 
2K_2.fastq


They both need their own channel.

>   Is it because of the reads or sth else?
>    

Can you post your actual command ?

> Is it better to manually set the distance? Thanks!
>
>    

Usually no, especially for such short outer distances / inserts.

> Best,
> CJ
>    

Thanks.

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