[mira_talk] Re: caf2gap
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 13 Sep 2011 19:42:35 +0200
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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