[mira_talk] Re: Selecting best contigs...
- From: Andrzej N <andrzej.k.n@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 4 Dec 2009 15:42:17 -0600
Hello,
Now I'm happy, I picked best contigs (which technically are twice longer
than genome I work on), I did a dot plot... and now I know how to do "by
hand" alignment.
I can tell that MIRA was rejecting to join contigs since some of sequences
were REALLY long (at the end of contig AND this was like 2 sequences), end
of this sequences didn't match other sequences from other contigs (but now
we talk about 50 of them!)... so when I align them, very small regions are
not matching, HOWEVER after that region EVERYTHING IS PERFECT.
I know, you probably saw this stuff all the time :), but for me learning
this "alone" is something new. I think I can put now my genomes "by hand"
and de novo. We will see.
Thank you and *I'm going* to bother you more ;).
Andrzej
On Fri, Dec 4, 2009 at 2:16 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> 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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