[mira_talk] Bivalve EST assembling
- From: Juan Fernandez Tajes <jfernandezt@xxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 3 Oct 2011 23:47:58 +0200
Dear all,
My name is Juan and I´d like to use MIRA for assembling an EST project. I have
450,000 454 FLX reads from a bivalve corresponding to a normalized library. I
have removed adapters and vector from reads before assembling. I have cleaned
them with cutadapt and seqtrimnext pipeline. I have read the manual for MIRA
and I thought to use these running parameters for the assembly:
-job=denovo,est,accurate,454 -highlyrepetitive -notraceinfo, are these
parameters appropriate??
It would be a better idea running a "draft", or "normal" assembly before an
"accurate" one? I have turned on the highlyrepetitive switch because it is
likely that these bivalves have sequences highly repetitive even in cDNA
sequences.
Many thanks in advance
Juan
---------------------------------------------------------------
Juan Fernandez Tajes, ph. D
Grupo XENOMAR
Departamento de Biología Celular y Molecular
Facultad de Ciencias-Universidade da Coruña
Tlf. +34 981 167000 ext 2030
e-mail: jfernandezt@xxxxxx
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