Splitting libraries based on the presence of two barcode sequences

[michael millican]

I am new to bioinformatic analysis of illumina sequencing (or any sequencing for that matter) data.

Question:

After I join my paired ends is there a way for me to split the pair end joined data and organize it based on the presence of one barcode at the 5' end and a different barcode at the 3' end?

Currently, I only see how to split my libraries based on the presence of only a single barcode sequence.

Thank you,

Michael