On Donnerstag 22 Juli 2010 Thomas Müller wrote:
Is the number of rep_c I receive too high for a cDNA library?
This question cannot be answered ... it's like: "Are there too many clouds in
the sky?"
Well, sometimes yes, sometimes no. Depends :-) But cannot be answered from
afar.
Have I made a mistake in the mira call (see below)?
mira --project=nnn -job=denovo,454,est,normal --notraceinfo -SK:not=10
-AS:urd=no -OUT:rld=yes -AS:sd=no -CO:asir=yes 454_SETTINGS -LR:mxti=no
-CL:qc=no -CL:cpat=no -AS:epoq=no -AL:mrs=90 -CO:rodirs=10 -SK:pr=80
-AS:mrl=50 -AL:mo=20 -FN:fai=nnn.fasta -FN:fqui=nnn.qual
Looks pretty good. -CO:asir will lead to clustering of homologues/paralogues.
In that case I would perhaps also try more stringent rules (-AL:mrs=95 -
CO:rodirs=5), though this will lead to even more contigs.
You may also be interested in trying miraSearchESTSNPs separately on each
strain and use the results from step3 to do your analysis.
Also try miraSearchESTSNPs with both strains at once :-)
B.
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