[mira_talk] Re: Removing a duplicate entry from a CAF file
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 13 Oct 2011 22:08:52 +0200
On Oct 13, 2011, at 21:46 , John Nash wrote:
> After sending me SIX genomes in casava 1.8 format, it appears that the
> SEVENTH genome came in the OLD format (as evidenced by the "/2" and "/1" at
> the ends of the lines of the headers). Of course, I didn't check and just
> popped the new sequence in the pipeline.
Uh ... I could not help but chuckle at that. I know I would have walked
straight into the same trap.
> My converter happily but incorrectly converted the headers - thus removing
> the "/1" and "/2" at the ends. That resulted in the error that
> convert_project threw
Were "duplicates" already in the input or did that now happen after MIRA?
> when I was trimming the CAF file to decent sized contigs. The sequence
> assembly looks really weird!
You know the -s option of convert_project? Together with -x, -y and -z it can
be quite useful at times.
On a slightly related note: I got my first CASAVA 1.8 data this week. 100GB
(packed). Fun. But this means that a name resolver for 1.8 style names /
comments will be written very soon ;-)
Luckily I learned about the /1, /2 and /3 reads today ... hadn't known Illumina
had changed their sequencing strategy.
B.
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