I have paired-end demultiplexed Fastq data with filenames in the following format for a single sample.
I believe that I could use the Casava 1.8 paired-end demultiplexed fastq protocol for importing this data. However, in place of barcode sequence/ or a barcode identifier, what I have is S3 in this example.
I had 56 samples in my Illumina MiSeq run and in place of a barcode identifier what I have is S1 – S56 from sample #1- sample #56.
Are these S1- S56 series considered as barcode identifiers for their respective samples? I was expecting an i5 or i7 combination here. Please let me know.