On Fri, 2012-02-03 at 11:22 +0530, Sushmita Mookherjee wrote: > Dear Sébastien, > > I have gone through the Ray URL and came to know about this software > regarding de novo assembly using raw reads. I used Ray-1.7 > successfully for my IonTorrent data (Organism E.coli) for both > overlapping paired end reads and single end reads separately. In > output, I found that for each run it generates one Contig and one > Scaffold file.
Yes. And a summary in OutputNumbers.txt > But for Scaffold, the number should be less than the Contig which I > found in paired end reads Scaffolds are basically ordered and oriented contigs. Scaffold S1 can for example be Contig C1 followed by Contig C2. To infer these relationships, paired reads are needed. > but for single end reads the number of Contigs are equal to the > number of scaffolds. Single end reads can not be utilised by Ray to do scaffolding. > Can you please help me to understand the logic? In addition E.coli > genome is around 4.6 Mb, but after de novo assembly I got the > assembled genome size is around 4.4 Mb. This is usually due to repeats being only there once in the assembly or simply that the quantity and quality of data does not permit a 100% breadth of coverage, regardless of the depth of coverage. > To improve the size which parameter I need to change .... Can you > please through some lights on this? > You can change the k-mer length, which is basically the only parameter in Ray. In controls the word size used to cut reads in small pieces. See this review for instance: http://www.nature.com/nbt/journal/v29/n11/abs/nbt.2023.html > Thanks and Regards, > > Sushmita Mookherjee I cc'ed my response to the list. ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
