[mira_talk] Re: New Solexa file format not supported by mira?
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Aug 2011 11:10:18 +0200
but they dropped qseq support ... so you need to either create them on your
own (OLB) or fix their fastq header.
It is probably not worth (yet) to include "illumina special fastq" support
into MIRA. Providing a simple "fix" utility should do the job.
my 2p,
Sven
2011/8/14 Dana Price <dana.price@xxxxxxxxx>
> 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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