Is there a way to remove 5' adapters using Trim Galore? I know that cutadapt has this capability, but does Trim Galore have this capability too? If not, any suggestion using the public Galaxy server how this could be done? Thanks
Thanks, Jennifer. I think this would be a helpful tool to have available for everyone who are not able to have their own Galaxy.
But to the point at hand, I solved the problem. First, I used "manipulate fastq" to reverse complement the entire fastq file. Then, I used Trim Galore! on the reverse complement of the 5'-adapter to trim it. Then, I used manipulate fastq again to reverse complement the file back again to the way it was. Then, I used Trim Galore! on the 3'-adapter to trim it.
It worked, but it was a lot of extra steps and time.
There currently isn't a tool available at Galaxy Main (http://usegalaxy.org) to trim 5' adaptors. For now, the original cutadapt wrapper tool is the available option (sourced from the Tool Shed for use in your own Galaxy).
I opened a ticket to request that this functionality be added the to existing Trim Galore! wrapper but some other solution may come up. Follow progress here: https://github.com/bgruening/galaxytools/issues/621
Thanks, Jen, Galaxy team