[mira_talk] Re: Bivalve EST assembling
- From: Juan Fernandez Tajes <jfernandezt@xxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 12 Oct 2011 16:40:18 +0200
Just for the record the reads were "cleaned" from vectors, adaptors,
polyA with seqtrimnext and cutadapt.
This is the output message on the screen when mira stops due to the high
percentage of megahubs, although I know that bivalve is highly
repetitive in DNA sequences
You have more than 0% of your reads found to be megahubs.
You should sheck the following:
1) for Sanger sequences: are all the sequencing vectors masked /
clipped?
2) for 454 sequences: are all the adaptors masked / clipped?
You will find in the info directory a file called
'*_info_readrepeats.lst',
consult the MIRA manual on how to extract repeat information from there.
*ONLY* when you are sure that no (or only a very negligible number) of
sequencing
vector / adaptor sequence is remaining, try this:
3) for organisms with complex repeats (eukaryots & some bacteria):
- reduce the -SK:nrr parameter (divide by 2)
4) for EST projects, -SK:nrr will not really work, use -SK:nrr (start at
10 and increase in steps of of 10)
*ONLY* if the above fails, try increasing the -SK:mmhr parameter
Note that the number of present megahubs will increase computation time
in
an exponential way, so be careful when changing -SK:mmhr.
El mié, 12-10-2011 a las 16:14 +0200, Juan Fernandez Tajes escribió:
> Hi all,
>
> I have launched mira with -job=denovo,est,accurate,454 -highlyrepetitive
> -notraceinfo, nevertheless, mira stops and warns me about megahubs in my
> read (approximately a 2%). The program and the manual suggest set
> -SK:nrr set to 10,
>
> Do you think that with these parameters will fix the problem:
>
> -job=denovo,est,accurate,454 -highlyrepetitive -notraceinfo
> -SK:mnr=yes:nrr=10
>
>
> Many thanks for the help
>
> Juan
>
> El jue, 06-10-2011 a las 00:04 +0200, Bastien Chevreux escribió:
> > On Monday 03 October 2011 23:47:58 Juan Fernandez Tajes wrote:
> >
> > > [...]
> >
> > > -job=denovo,est,accurate,454 -highlyrepetitive -notraceinfo, are
> > these
> >
> > > parameters appropriate??
> >
> >
> > If you're not looking for something special, yes.
> >
> >
> > > It would be a better idea running a "draft", or "normal" assembly
> > before an
> >
> > > "accurate" one?
> >
> >
> > Not really.
> >
> >
> > B.
> >
>
>
>
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