Re: [wgs-assembler-users] Input a library with wrong orientation, can I edit gkp?

[Walenz, B. <bw...@jc...>]

Hi, Ole-

Very sorry to hear.  I've been stung by this a few times too.

There is minimal support for non-innie oriented mates.  The assembler was
developed with innie-oriented mates assumed, and there are still lots of
places where we make that assumption.  In particular, finding evidence for
merging two scaffolds assumes innie oriented mates; computing gap sizes
based on mate pairs also does.  Both explicitly exclude non-innie oriented
mates from contributing.

The same issue comes up after classifyMates runs.  We're left with a pile of
now outtie-oriented PE pairs that we can do nothing with.  We thought about
updating the stores (reverse complementing the read), but as every overlap
involving these reads would need to be modified, we decided this was just
too risky.

So, I'm sad to say, recomputing is the only real option.  If it makes you
feel any better, I had to run overlaps on a big assembly three times because
our scratch disk policy is to delete files older than a week, and I kept
getting pulled away from it.

You might be able to learn something from this run though.  Bogart can't use
all 3.3tb of those overlaps, so maybe you can reduce the number of overlaps.

Is the minimum overlap length too low?  You could spot check some overlaps
to see what the longest overlap is.  You might be able to get away with,
say, a minimum overlap length of 64 bases.

Is the error rate too high?  Again spot checking, are there reads with no
low-error overlaps?  Maybe you can get away with only 4% error.

b



On 8/10/12 3:18 PM, "Ole Kristian Tørresen" <o.k...@bi...> wrote:

> Hi,
> I ran classify on an Illumina mate pair library, and managed to use
> one of the old versions of gatekeeper to dump the reads, so I guess
> they were dumped as innie reads. I thought the library still was
> outtie, and input that into an assembly. Now, after finishing
> overlapper (using grid and grid version of overlapStoreBuild) I have a
> ovlStore of 3.3 TB, so I'd rather not run that again if I can avoid
> it.
> 
> I see from this page:
> http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Gatekeeper
> #Library
> that there are some options in changing orientation of the library,
> but only "innie" is supported it says. Do you have any suggestions of
> what I can do? Would it not work changing the library to "outtie"?
> 
> Thank you.
> 
> Ole
> 
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