[mira_talk] Re: Filtering out crappy sequence
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 4 Apr 2012 22:59:49 +0200
On Apr 4, 2012, at 22:04 , John Nash wrote:
>> It would be worth testing the SFF file in other tools (e.g. the
>> Roche applications or Biopython) to isolate the problem.
>> If all the problem reads show this pattern (all their read
>> qualities are PHRED 1) that should be easy to filter out.
>
> I was just downloading some other converters to do that as your email came in
> :)
I'll second Peter: look what other converters have to say. My first stop would
by the Roche sff_dump if you have (or whatever it is called).
In case the SFF has, like the FASTQ, no sequence, then I think your provider
has a problem (and they should be notified). In case the SFF looks OK, then
either Jose or myself should have a look at that SFF to see what kind of
weirdness broke sff_extract.
B.
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