I have the multiplexed paired-end read files from an Illumina run and I have both forward and reverse index files. I have figured out I can use barcode splitter to split the read files individually, but how do I get the set of sequences associated with the unique F/R barcode combinations to match each sample? For example, I have 8 samples with the same forward barcode/index 1 but they each have a different reverse barcode/index 2. How do I split that data into 8 separate files?
For advanced manipulations, you can use the Apply rules tool.
This is super flexible, so a bit complicated, but once you do it, you’ll learn what it can do. See the tutorials linked on the form for examples and a walk-through.
Once you data is in a paired-end collection folder with sample labels, you can use the data organized that way or rearrange the collection shape or even get the data out of the collection folder all using other Collection Operations tools (each also have a tutorial).
These are the core of working with data in an organized way. Most of the published Galaxy workflows will include collections, too, for even more examples.
Please give that a try, and we can follow up if you get stuck if you share back what you have so far with a shared history link. How to generate it is in the banner at this forum, and you can paste that link back here and explain what part isn’t working. Hope this helps!
