[mira_talk] Re: New Solexa file format not supported by mira?
- From: Dana Price <dana.price@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 14 Aug 2011 12:12:07 -0400
I've been converting the Illumina .qseq files to .fastq with a perl script
ever since we purchased the instrument. It just makes life easier.. no
Q-scoring/header formatting issues to worry about. I can't stand all the
changes they've been making to the BUSTARD output with each new version.
Dana
On Sun, Aug 14, 2011 at 11:16 AM, Robert Bruccoleri <
bruc@xxxxxxxxxxxxxxxxxxxxx> wrote:
> **
> Dear Colleagues,
> One important thing to keep in mind when the new format is used -- the
> Illumina 'chastity' filter is encoded in the second field of the second word
> of the header line. In the past, the instrument would remove sequences which
> failed to pass the filter. Now, those reads are included. You have to decide
> whether you want to use the additional reads.
>
> Bob
>
>
> Bastien Chevreux wrote:
>
> On Aug 13, 2011, at 20:40 , Peter Cock wrote:
>
>
> Do i have to change all @headers now??
>
>
> Yes, unless Bastien has already updated the latest version of MIRA
> to cope with the new Illumina 1.8 files.
>
>
> I haven't. Will probably do whenever I encounter a 1.8 pipeline data set for
> the first time. But I'm still wondering why Illumina made that change in the
> first place, I cannot find a single good explanation.
>
> In the mean time, changing the @-header lines is left as an exercise to the
> reader :-)
>
> B.
>
>
>
>
>
>
--
Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu
d.price@xxxxxxxxxxx
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