On Tue, Oct 4, 2011 at 1:33 AM, Colleen Doherty <cdohe...@ucsd.edu> wrote:
> I am trying to set up a local instance.
> When running Clip adapter sequences I get the following error:
>
> fastx_clipper: Invalid quality score value (char 'J' ord 74 quality
> value 41) on line 36
> gzip: stdout: Broken pipe
>
> I'm stuck on where to try to trouble-shoot this.

You need to upgrade to at least FASTX Toolkit v0.0.13, see:
http://seqanswers.com/forums/showpost.php?p=49667&postcount=18

Old versions wrongly assumed PHRED quality scores would be at most 40.

Peter
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