On Tue, Feb 21, 2012 at 5:49 PM, Borrone, James
<james.w.borr...@okstate.edu> wrote:
> hello,
> I am trying to use the FastX tools on the Main server to trim and manipulate 
> FASTQ files extracted directly from an sff file (again using the main galaxy 
> web server).  In using Clip and the Reverse compliment tools, I get the 
> following error:
> An error occurred running this job: fastx_reverse_complement: (or fastx_clip) 
> found invalid nucleotide sequence 

When you turn the SFF into FASTQ, ask for the trimmed reads. That
will remove the lower case nucleotides.


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