[mira_talk] Re: Assembly after vector screening
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 31 Aug 2011 15:16:42 +0200
On Aug 31, 2011, at 14:04 , Nestor Zaburannyi wrote:
> Version 3.4 final. Bacteria. 146 bp. Average coverage is 37.
Sensible parameters. Never worked with reads that long though, but looks
sensible.
> My vector is in my vector.fasta, in fasta format.
I figured :-) Just wanted to know whether that contains Illumina specific
sequences MIRA is already searching for.
Back to your problem: under no circumstances should this high number of
unresolved repeat markers (SRMc) be found at the end of a regular "accurate"
assembly. A handful, OK. One or two dozen ... yeah well, shit happens. But
almost 2000? No way.
There must be another effect there. Did you have a look at a couple of
SRMc/IUPc markers of the contigs in an assembly viewer to see if there is a
pattern?
I could have a look at it if you want, but that'll not be immediately as I'm on
vacation right now.
Best,
Bastien
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