Hi, I have received fastq files containing the reads from Illumina MiSeq. Since they are paired-end, there is an R1 and an R2 file for each sample. So I expected to find reads beginning with our forward primer in the R1 files, and reads beginning with our reverse primer in the R2 (or vice versa). However, I find both in both; i.e. about half of the reads in the R1 files begin with the forward primer, and half with the reverse primer; and same with the R2s. I tried merging them, but this results in about half of the reads being reverse complemented, and this makes things more complicated downstream, so I would like them to all go in the same direction. I thought to grep for each of the primers, but because of ambiguities and some still having short tags on the beginning, I don't think it's going to work--plus I thought they weren't supposed to be mixed anyway...??? Maybe I don't understand this as well as I thought. Any ideas? Thanks.