[mira_talk] Re: Bivalve EST assembling
- From: Juan Fernandez Tajes <jfernandezt@xxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 12 Oct 2011 19:08:55 +0200
I got Mira to work but I had to increase, mmhr=3, I hope I didn't do
anything wrong, although Bastien warn in manual about modifying mmhr.
The problem is after Mira has finished I got a number of all contigs too
high, All contigs=34276 contigs, and I think this number is too much for
250641 reads assembled, any clues about what is happening?
Many thanks in advance and sorry for so many posts
Juan
El mié, 12-10-2011 a las 16:40 +0200, Juan Fernandez Tajes escribió:
> 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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