Hello Biostars Community,

General question(s) here, specifically in regards to sequencing platforms and some related questions on sequencing, as well?

1. Could using a newer/the newest computational genome/annotation (for example, presently, Ensembl 107 or the newest Gencode version) adversely effect the actual truth of what was sequenced?

2. When sequencing is done through an Illumina machine or other big name company machines, are those sequencing platforms *completely independent* from the genome or DNA/cDNA being sequencing?

3. What happens if, for example, "famous gene ABC" and "low-profile gene XYZ" are found to have different 3' and/or 5' ends by some new discovery, in Illumina, would adapters still link to them to perform those bridge PCR reactions on the flow cell lanes, or would it be that all the data published before on "famous gene ABC" and "low-profile gene XYZ" should be revisited? Or is it like question #2, "completely independent" - are even adapters independent from genes?

I was doing some reading, and I guess the gene sequence really only matters for probe-based sequencing (chips and arrays?). Hopefully this question could be a good resource for others?

Thank you in advance.
- Pratik
Excellent responses by  GenoMax to wonderful questions by Pratik.  I echo what GenoMax says. 

IMHO, the platforms ar einherent to capture technologies as well. NOT necessarily or everytime one would intend to use the same samples with different sequencing platforms/technologies unless the lab is rich.  Even otherwise, I wouldn't recommend that.  Taken together, the need of the our is to emply machine learning heuristics and predict such outcomes on a large scale.   Could completely independent be dependent can give some interesting reasons for us to explore. 

Just my two cents
Prash 