On Tuesday 25 January 2011 16:59:40 Zhao Lai wrote: > We have been using MIRA for 454 transcriptome sequences assembly for a > while. This is the first time we use the new version (version3.2.1) to > assembly one full plate of 454 titanium normalized EST data. Surprisingly, > there is no singlet in the output! Everything has been assembled to contig. > > The command we used for the 454 EST assembly: /nfs/bio/sw/bin/mira > -project=ISI -fasta -job=denovo,est,accurate,454 -noclipping -notraceinfo > 454_SETTINGS -AS:mrl=50 -AL:mrs=94 -OUT:sssip=yes -CL:bsqc=yes. I checked > the manual and saw this part: "-OUT:sssip=yes" which I assume this should > send all singlets to the results, and it's the same command I used before > for other EST 454 sequencing assembly project with the old version . So I > can not explain why there is no singlets for this assembling. Don't know > whether the new version is the reason. From the manual under http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_output_out [savesimplesingletsinproject(sssip)=on|yes|1,off|no|0] Default is no. Controls whether 'unimportant' singlets are written to the result files. [Note] Note Note that a value larger 1 of the [-AS:mrpc] parameter will disable the function of this parameter. -AS:mrpc is set to values larger than 1 for most default assembly types (the output log should tell you that also when in doubt for your special parameter combination). Does this help you? B. -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html