[mira_talk] Re: How many passes to use.....
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 14 Nov 2013 13:05:08 +0100 (CET)
> On November 14, 2013 at 12:21 AM Torben Nielsen <torben@xxxxxxxxxx> wrote:
> I'm about to start another run which will go for a week or two. These are the
> parameters I am giving it:
Whether you assemble the metagenome data in genome or EST mode would have been
interesting.
> parameters = -SK:not=16:pr=95:mchr=8192 \
> -CL:asjdc=yes
I'm feeling uneasy about -CL:asjdc as sometimes it clips way too generously and
I have not found out yet. That's one of the reasons why it's generally switched
off by default.
> -AS:nop=6:mrpc=2 \
> 454_SETTINGS -AL:mrs=95 \
> 454_SETTINGS -CL:qc=yes:pec=yes
Careful with -CL:qc as 454 base qualities somewhat shifted over the years. Worst
case: too generous clipping. I normally keep the clips coming off the 454
pipeline.
B.
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