I know these are very basic questions and sorry if these sorts of things are too basic or redundant and have been answered elsewhere a while back, but I have not been able to find straightforward answers in this forum or elsewhere, so would appreciate your help.
1) What is the definition of a "read?" Is a read the number of clusters with DNA molecule fragments from the same library (sample) or is it the total number of DNA molecule fragments from the same library? Or is it something else altogether?
2) Can someone tell me the total number of clusters on a lane of a MiSeq flow cell? Also, on a lane of a HiSeq 2500 and HiSeqX flow cell?
3) Lastly, say I am doing a study - PE150 sequencing (so sequencing 150 bases in from each end on each fragment) for 96 samples (libraries) which I want to run out on a single lane of a HiSeq 2500. This would translate into 1.5-2 million reads/library. What would be the difference in data generation and/or advantage/disadvantage if I did the same thing except with PE300 (so 300 bases in from each end)? Is the only difference the cost in price of the chemistry used to generate the reads? i.e. PE300 would sequence the fragments for longer and cost more and also generate more data, so the reads are more likely to be more precise? The total number of reads as I understand it would remain the same. Right? So it is more of a matter of - do I want to spend the extra money to identify and later map each DNA fragment with greater precision - right?