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
A newer genome annotation/curation would be **independent** and not affect the actually nucleic acids sequenced  by the machine (unless they were captured using a targeted approach **prior** to sequencing - e.g. whole exome sequencing). Whole genome sequencing will include ALL fragments present (regardless of genome/annotation) - assuming they are physically "able to be sequenced" (see homopolymers, etc... in the comment above).

**Adapters are independent of genes**

>  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?

You are correct
