[mira_talk] Re: MIRA run failing due to megahubs
- From: Martin MOKREJŠ <mmokrejs@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 25 Jun 2014 19:44:12 +0200
But in transcripts there shouldn't be CA repeats, or GATC, etc. ;) I agree, in
genomic data reality
is different so you may eventually succeed to assemble even these simple
repeats.
M
Jose Huguet Tapia wrote:
> "But the point is not to overcome the error message and keep the crap in the
> dataset but to either properly
> clean the input data or to drop it and make the life easier to the assembler.
> It is also faster so "forget
> this possibility". ;-)"
>
> depends if the 'crap" is real "crap" or is a real composition of a complex
> genome. Of course depends the types of repeats that you have in your list.
>
>
>
> On Wed, Jun 25, 2014 at 12:59 PM, Martin MOKREJŠ <mmokrejs@xxxxxxxxx
> <mailto:mmokrejs@xxxxxxxxx>> wrote:
>
> Jose Huguet Tapia wrote:
> > Hello Victoria,
> > I believe that you could set the megahubs limit to a 1.
>
> But the point is not to overcome the error message and keep the crap in
> the dataset but to either properly
> clean the input data or to drop it and make the life easier to the
> assembler. It is also faster so "forget
> this possibility". ;-)
>
> > add
> >
> > -SK:mmhr=1 (for 1 % megahub accepted)
> >
> > Which version are you using? I work with V 4.0. and I found that the
> megahub limit is set up to 90. I do not if this right. Maybe Bastien could
> have a suggestion. My case seems to be more dramatical!. I have more than 90
> > Thanks
> >
> > On Wed, Jun 25, 2014 at 11:36 AM, Offord, Victoria <vofford@xxxxxxxxx
> <mailto:vofford@xxxxxxxxx> <mailto:vofford@xxxxxxxxx
> <mailto:vofford@xxxxxxxxx>>> wrote:
> >
> > Hi, ____
> >
> > __ __
> >
> > My MIRA run on a parasite transcriptome keeps ending with:____
> >
> > __ __
> >
> > You have 0.1052271917% of your reads as megahubs.____
> >
> > You have set a maximum allowed ratio of: 0.0000000000____
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