Is there a program that I can take my paired fastq files, and break them into smaller files. Say I have a 150mb pair, and I want to split it into 5 x 30mb pairs??
Hi,
have you tried toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
It doesn’t support PE data explicitly, so better check the output carefully, but I’d assume it would do the right thing.
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I see the program in the toolbox for downloading, but can it be used in Galaxy???
Hi @Jon_Colman
Maybe I can help. You can find this tool under Collection Operations in the tool panel at a UseGalaxy server.
- Split file to dataset collection
This can consume a collection but you may need to run these other tools if your pairs are in a paired end collection (both ends nested under the sample identifier). Just be sure to use consistent options with the Split file tool to apply the same criteria to both.
- Unzip collection → Split file to dataset collection (on both ends) → Zip collection
More manipulations: GTN Materials Search. But also see the tool forms. Most have a graphic that explains what each do. If you get stuck, you can share back your data in a history and we can help with the exact steps.
Hope this helps! 
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