For vector removal i tried several things, NCBI Univec, etc.. What about 454 adapters? ________________________________ From: Visam Gültekin <teutara@xxxxxxxxxxx> To: Mira Talk <mira_talk@xxxxxxxxxxxxx> Sent: Thursday, September 29, 2011 11:49 AM Subject: [mira_talk] Re: awkward letters in assembled data That is right, there is no .qual file. For vector removal i tried several things, NCBI Univec, etc.. It seems different preprocessing steps outputs -more or less- same results. For that reason i am almost confident that the reads i have are clean, but still no .qual file. mira --project=run4 --job=est,accurate,denovo,454 -notraceinfo >454_SETTINGS -AS:epoq=no -CL:qc=no:cpat=no >-AL:egp=no -LR:wqf=no:lsd=1:ft=fasta -CO:fnicpst > will be my best shot i guess? V.G. > Subject: [mira_talk] Re: awkward letters in assembled data > From: bach@xxxxxxxxxxxx > Date: Thu, 29 Sep 2011 20:44:03 +0200 > To: mira_talk@xxxxxxxxxxxxx > > On Sep 29, 2011, at 20:39 , Peter Cock wrote: > > That suggests you have FASTA sequences (are there > > matching QUAL files with quality scores?). > > I have the bad feeling that there are no qualities. > > Vi sam, in that case you *do* want to read about assembly without qualities. > > 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