3.2 years ago by
The Fastq dataset merging tool in Galaxy do not address overlap resolution. This are a straightforward merge: end-to-end.
If there a reason why you want to do this at the start of the experiment? The NGS mapping tools wrapped for Galaxy and available on the public Main server at http://usegalaxy.org are designed to work with pair-end reads given as individual dataset inputs. There are both technical and scientific reasons why this is desirable.
Please share more about what you are trying to accomplish downstream (perhaps include target tools or workflows) if this does not help. If the question is broad and involves many details, please start up a new post. You can always link this one in for reference. One question per-post is the best way to organize information at this support forum.
Just for reference, please see the Learn/GalaxyNGS101 for the most common workflow procedures utilizing the tool sets hosted on http://usegalaxy.org. There are many other tools and pipelines (sourced from the Tool Shed for a local/cloud Galaxy and/or hosted-executed on other public Galaxy servers with domain focus), but guessing which is applicable for your research isn't the best way to help you move forward with your analysis goals.
Thanks! Jen, Galaxy team