Dear Galaxy team I am so sorry for repeatedly posting the same question, but I do need some inputs in to this. Please let mek now the best way to use barcode splitter on Paired end Miseq data. The data is already split for the Illumina indexes using Miseq reporter, what I want to do is to split some inhouse barcodes within each of the sample. Barcodes are there in both 5' and 3' end but they are both the same. Please let me know if the best practise is to 1. Join read 1 and two - barcode split and split the two reads 2. Split Read 1 and 2 and them join using FastQ joiner and split again Basically I want to exclude any reads where the same numbered reads are not categorised in to the same barcode. Thanks Kind Regards, Veranja Veranja Liyanapathirana Graduate student Microbiology, CUHK