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
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,
option is located in Manipulate Reads -> Manipulate on 'Sequence
Content' -> Sequence Manipulation Type:. There are several options
including trim again, but also "Reverse Complement".
Hopefully this helps!
This Galaxy wrapper is based on the FASTX-Toolkit tool by the same
A link to the original is at the bottom of the tool's form in the UI.
see the Galaxy wrapper, it is in the source here: galaxy-central /
Questions about the core tool can be directed to the tool author. Help
with running a local Galaxy or tools in general is on the
email@example.com mailing list:
If you create a new wrapper with more options, please consider
contributing it to the Tool Shed, as this tool is super popular and
option for 5' clipping has come up before.