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 ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users