Import sequence data that contains R1 , R2, and the corresponding barcode

[ben (benjamin w.)]

Hi all, I had the same questions, you can check my thread:

Weird Illumina MiSeq question, some help with import?

Hi @ben, The issue is simply that the file names are incorrect for EMP format, even though the format is correct. Try this: Make a new directory raw-seqs run the following commands (you will probably need to change the filepaths): cp lane1_NoIndex_R1_001.fastq raw-seqs/forward.fastq.gz cp lane1_NoIndex_R1_002.fastq raw-seqs/barcodes.fastq.gz cp lane1_NoIndex_R1_003.fastq raw-seqs/reverse.fastq.gz Try importing again as EMP format Let me know if that helps!