On 03/11/11 09:30 AM, CJ wrote: > Hi Seb, > > The following is my command setting: > ------------------------ > mpirun -np 8 \ > Ray \ > -k \ > 21 \ > -p \ > AR500.filter80_1.fastq \ > AR500.filter80_2.fastq \ > -p \ > AR2K.filter80_1.fastq \ > AR2K.filter80_2.fastq \ > -amos \ > -o \ > Raytest > ------------------------ > Then I got the somewhat strange estimate of outer distances in the > LibraryStatistics file > > By the way, what kind of quality trimming for the solexa reads would > you recommend to feed Ray? > > Best regards, > CJ > > > 2011/11/3 Sébastien Boisvert<[email protected]>: > >> 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. >> >>
Your command is correct. Can you post Library0.txt and Library1.txt ? ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
