[mira_talk] Re: caf2gap
- From: Brian Forde <bforde@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 14 Sep 2011 08:59:43 +0100
Thanks Everyone,
I willl use gap5. It seems to be far more stable now than the last time I
used it and the template display actually works.
regards
Brian
On Tue, Sep 13, 2011 at 6:42 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Sep 13, 2011, at 14:46 , Robert Bruccoleri wrote:
> > The problem is the large size of the CAF file. There are two other
> possibilities. First, use convert_project to reduce the number of contigs in
> the caf file, e.g.:
> >
> > convert_project -f caf -t caf -x 2000 -y 10 source.caf dest
> >
> > will make a new CAF file with only contigs bigger than 2000 bp.
>
> Brian is doing a mapping, I have my doubts that the strategy of filtering
> only for large contigs will work. BTW, using MAF as input for the conversion
> is faster and uses a bit less memory.
>
> > Second, use cafcat and the -fofn option to select contigs of
> interest.
>
> Ummm, yes, cafcat is a possibility. Which I never use: "convert_project -n"
> does the same there.
>
> Brian: you might nevertheless want to try the splitting approach. In fact,
> for many chromosomes/contigs of your reference sequence that should work.
> However, in case the reference sequence has collapsed repeats (I've seen
> reference sequences with just one rRNA copy as placeholder for >100 rRNA
> copies across the genome), you might still have the caf2gap problem for that
> chromosome/contig if that repeat is quite polymorphic.
>
> If that's the case, just drop a note here and I'll jot down an undocumented
> trick which I developed to get around that problem.
>
> B.
>
>
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