I have Rad tag data that I'm trying to map to our reference genome in
Galaxy on our local instance. After barcode splitter, I have 96 files
(one each of all of the sequences for that individual). It seems like
the current tools (e.g. bowtie) can only map a single file to the
reference. I think that even if I were to do this step 96 times, I
would still end up with 96 files at the end and not the linkage map
that I hoped for.

Any ideas on how to move forward from this stage?
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