[mira_talk] Re: Removing a duplicate entry from a CAF file
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 13 Oct 2011 15:55:55 -0400
On 2011-10-13, at 3:46 PM, 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. 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 when I was
> trimming the CAF file to decent sized contigs. The sequence assembly looks
> really weird!
>
> Moral: Check your fastq formatted sequences EVERY time after downloading from
> the sequence provider.
Upon further checking, the sequencing centre appears to have converted the file
header itself because it uses the new style flow-cell IDs and Sanger offsets
for quality. Hmmmmm.
Check your raw data mes ami(e)s.
John
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