[mira_talk] Re: Selecting best contigs...
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 4 Dec 2009 21:16:44 +0100
On Freitag 04 Dezember 2009 Andrzej N wrote:
> Large contigs:
> --------------
> With Contig size >= 500
> AND (Total avg. Cov >= 29
> OR Cov(san) >= 0
> OR Cov(454) >= 27
> OR Cov(sxa) >= 0
> OR Cov(sid) >= 0
> )
>
> Length assessment:
> ------------------
> Number of contigs: 169
> [...]
> I would like to choose ONLY this 169 contigs to work on it in GAP4. I know
> how to choose contigs based on size, but how can I get this 169 contigs in
> ONE file?
MIRA chose minimum length of 500 bases and a minimum average coverage of 27 to
say that a contig is 'large'.
To extract those reads from the CAF (or MAF) file, use convert_project with:
convert_project -f caf -t caf -x 500 -y 27 input.caf output
and then you can use "output.caf" with caf2gap to get those contigs into gap4.
Except when choosing EXP format as output (-t exp), the result will always be
in one file.
> There 894 coverage, this is because there are repeats which pile up on each
> other, is there any option to "stop" MIRA of doing it?
Hmmm, -AS:ard should've take care of that. Will need to check.
Regards,
Bastien
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