[mira_talk] Re: Singlets after hybrid assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 6 Sep 2009 17:33:24 +0200
On Sonntag 06 September 2009 Andrew Gracey wrote:
> Thanks in advance for any insights you can offer.
Hi Andrew,
I suppose the "missing" reads got filtered out one way or the other and have
landed in the debris. This could have happened in clipping or during the SKIM
phase if your library was not normalised (as I guess it wasn't). To say more I
would have to look at the 'live' data.
"unimportant" in the description of -OUT:sssip is geared towards singlets in
genome assemblies. In short, these reads qualify as "unimportant":$
- reads without any overlaps
- reads too short
- reads "left over" after assembly,i.e., they have overlaps but were not
accepted into contigs during alignment
- megahubs: reads with so many potential overlaps that it's almost useless to
try. Often seen in non-normalised EST libraries.
Reads that did not make it into contigs/singlets are listed in the debris
file.
While checking your command line, I noticed an oversight: the quickswitch
combination you used does not switch on poly-AT clipping for 454 reads as it
should. This could explain megahub status for a number of reads. I fixed that
in the current development code. In the mean time, could you please try the
following command line:
./mira -project=Bot -job=denovo,est,normal,sanger,454
454_SETTINGS -CL:cpat=on
>&log_assembly.txt
Regards,
Bastien
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