[mira_talk] Re: paired_end

On Tuesday 14 April 2009 Lionel Guy wrote:
> On 14 Apr 2009, at 16:08 , Jan Paces wrote:
> > Unfortunately it looks like it
> > is not possible to download .sff files from NCBI trace archive
> > anymore,
> > they are offering only fasta or fastq

It's not anymore? Oh hell, that would be a shame. Need to check that.

> I think there are some other utilities in the third-party tools of
> mira, although I don't know how they work. AFAIK, I have split my
> reads, using .r and .f suffixes. The xml file then resembles:

Yep, that's what it looks like. Ideally suited if you have multiple library 
sizes.

If you happen to have only *one* library size per sequencing technology, you 
can still use -GE:tismin and -GE:tismax.

E.g. to set up library size of 10k+/-3k for Sanger and 3k+/-1k for 454: 
     mira ... --job=...,sanger,454 
             -GE:tismin=7000:tismax=13000 
            -454_SETTINGS
             -GE:tismin=2000:tismax=4000 

Regards,
  Bastien


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