2.4 years ago by
It appears that replicates were concatenated together in the shared file (assumption). Try leaving these as distinct datasets and join the fastq for the paired sequences between lanes in these first, then proceed.
Depending on the analysis, you may want to combine R1 and R2 into the same read by overlap and/or combine directly (sometimes with a buffer region between the two). Other analyses work best with R1 and R2 entered distinctly on the tool form. Tools in Text Manipulation offer many options for this type of manipulation.
One example of doing this is in a training session that was presented just a few days ago for a Metagenomics pipeline at GCC 2016. See it here: https://gcc16.sched.org/event/5Y0M/metagenomics-with-galaxy
All training sessions at the conference are available on-line, complete with the video taping of the session. Review others for those that match your analysis goals. More training resources are linked at the top of the Galaxy Support wiki: https://wiki.galaxyproject.org/Support
Good luck! Jen, Galaxy team