Dear Bastien, Thanks for the quick response. Actually I'm waiting for your reply to conform one assembly to proceed forward. So my question is: do I have to perform the MIRA assembly again by changing the parameters or actually the singlets information is somewhere in the output folder and I can just go to grab them in the previous assembly folder? Thanks Zhao On Tue, Jan 25, 2011 at 1:37 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote: > 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 >