[mira_talk] no singlets on the 454 EST aseembly?
- From: Zhao Lai <zhaolai2008@xxxxxxxxx>
- To: mira_talk <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 25 Jan 2011 10:59:40 -0500
Dear Bastien,
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.
I will really appreciate your answer for this.
Thanks
Zhao
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