[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.


You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 

Other related posts: