On Mon, 2012-02-20 at 13:31 -0500, Allen, Benjamin S wrote:
> Hi Sébastien,
> 
> With large insert Illumina PE libraries that are 3'-5'-5'-3' orientation, 
> does Ray automatically 
> handle this data or do you have to reverse complement the data before passing 
> it to Ray?

Ray deals with that.

>  For example 
> with SOAPdenovo you need to specify reverse_seq=1 for the library.
> 
> In addition, based on a few mailing list posts, it seems that with larger 
> insert library data one 
> should manually specify averageOuterDistance and standardDeviation for the 
> data. 

It really depends.

I would say that > 10000 Ray may not detect the peaks because it uses
the assembly seeds to do so.

> Just so I'm clear, 
> averageOuterDistance = pairLength x 2 + insert length.

Yes, it is the gap length + the read lengths.

>  For example for 150x2 with 326 insert length, 
> the averageOuterDistance = 625 = 150 * 2 + 325. 

Yes. But there are several definitions of 'insert length'.

> Do you know of a good way to identify standardDeviation 
> for a dataset?

Usually, it is < 10 %.


With Ray, there is a file called LibraryStatistics.txt.

It contains this information. And it works fine for insert lengths <
10000. The frequencies are in files Library<x>.txt.


If you have very large inserts, just provide 10% of the value for the
standard deviation.

> Either from the instrument or otherwise? 

You can use Agilent Bioanalyzer but usually, running software on the
data is more precise.

> For example in SRA, most libraries state the nominal
>  standardDeviation as 0. 
> 

I think 0 means unknown here.

Another way is to map reads onto a reference.

> Thanks,
> 
> Ben

Seb



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