For illumina platform, after the reads bind to the chip and bridge amplified, machine reads each read from top to bottom. I am wondering how does this top-bottom order transfer to fastq files. Does it become left to right? In anther word, (assuming index sequence shows in the naming line of fastq, not with the read.) the adaptor that is close to the bottom of chip, will be at the right end of each read (assume this adaptor gets sequenced).
Thank you very much.