[mira_talk] unwanted clipping
- From: <mark.rose@xxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 26 May 2011 18:39:59 -0400
I'm experimenting with mira for doing assemblies of Velvet contigs without
quality values. I saw the warning in the mira reference about attempting this
and so included reverse complements of my contigs as suggested and used the
following command line
mira --project=mira --job=denovo,genome,normal,sanger --fasta COMMON_SETTINGS
-CL:pec=no SANGER_SETTINGS -LR:wqf=0 -AS:epoq=0 -CL:emlc=0
I've also tried this supplying mira with a fake fasta quality file and using
the following command line
nohup mira --project=mira --job=denovo,genome,normal,sanger --fasta
SANGER_SETTINGS -CL:emlc=0
While both of these assembled there is still some clipping of the sequence
occurring and at the beginning and end of contigs. Do you know why and with
what settings I can prevent it?
Thanks much
Mark
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