[mira_talk] Re: How many passes to use.....
- From: Torben Nielsen <torben@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 14 Nov 2013 05:47:16 -1000
Bastien,
> Whether you assemble the metagenome data in genome or EST mode would have been
> interesting.
It's done in genome mode. Do you see any advantage to treating it as EST?
>> 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.
Thanks. I'll try a smaller test run with it off to see what happens.
>> -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.
You suggested somewhere before that the 454 pipeline clips are pretty good. So
for all of my data, I went back to the SFF files and used 'sff_extract -c' to
extract the data.
Thanks, Torben
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
