On 21/10/13 11:11 PM, Adrian Pelin wrote: > Hello, > > I tried an assembly with paired and and mate pairs: > mpiexec -n 32 Ray \ > -k \ > 89 \ > -p \ > /shared/reads/GDR-16_R1.NoAdaptPR.fastq \ > /shared/reads/GDR-16_R2.NoAdaptPR.fastq \ > 283 \ > 20 \ > -p \ > GDR17_NoPseudomonas_R1_RC.fastq \ > GDR17_NoPseudomonas_R2_RC.fastq \ > 2397 \ > 649 \ > -o \ > Miseq_MP_k89 > > The MiSeq paired end are 250bp each, so they overlap a lot since the fragment > is 283. The Mate pairs however are 100bp, and are likely contaminated with > paired end. I supplied this command, and the assembly did not return very > good stats. > > Should I maybe try the Mate Pairs without a predefined distance, and see what > Ray estimates the fragment size to be?
Did you check the content of LibraryData.xml (which contains paired end signals detected in the data) ? > > Is there any way to find out what the problem is? I know that by doing an > assembly on just the MiSeq with high kmers (above 200) I get better stats. Since your reads for mate pairs have 100 bp, using a k valued at 89 may discard some of the mate pair reads because mate pair data sometimes contain adapters (like the adapter used to circularize your material). > > Adrian > ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
