Hello,

The "Clip" program only acts on the 3' end. In some cases, running "FastQC" to isolate adapter regions, then using a tool like "FASTQ Trimmer" or "Trim" will work (if the lengths are somewhat fixed).


Alternately, the tools "NGS: QC and manipulation -> Reverse-Complement or Manipulate FASTQ" will reverse compliment reads. For the second, the option is located in Manipulate Reads -> Manipulate on 'Sequence Content' -> Sequence Manipulation Type:. There are several options here, including trim again, but also "Reverse Complement".

Hopefully this helps!

Jen
Galaxy team


On 8/22/13 12:03 PM, William Yarosh wrote:
Hi,

I was using the clip program, but my adapters are on the 5' end.  Is there any 
way to use this program so it will clip the 5' end or a way to make all my 
reads the reverse complement and run it through this program?

Thanks
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