Re: [galaxy-dev] FastX tools

On Tue, Feb 21, 2012 at 5:49 PM, Borrone, James <james.w.borrone@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 (gactGCGACTCACGTACAGCAATGCACATACTATATTATATC) on line 2

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