Dear Galaxy team,   I am sorry for repeatedly asking this question but I would like some feed back from anyone who has used barcode splitter on paired end reads as the different alternatives I used do not give satisfactory results in terms of expected read alignments. I have a set of Illumina Miseq reads with inhouse barcodes that I need to de maultiplex. It is esstential to make sure that the read 1 and read 2 are split to the same group and in instances that this condition is not fulfilled, the reads to be discarded. I tried to 1. Join read 1 and read 2 and then run barcode splitter, followed by FASTQ splitter 2. Use barcode splitter on read 1 and read 2 separately and use FASTQ joiner on the results to exclude instances where R1 and R2 are in different reads followed 3. Use barcode splitter on R1 and R2 results and straightaway use Bowtie for illumina for mapping   The results I get in the three methods are not compatible with each other. I would like to know the best method from the experience of other users on what the best method using Barcode splitter on Illumina Paired end reads,   Thank you, Kind Regards, Veranja   Veranja Liyanapathirana Graduate Student CUHK