Difference between lower and upper case N in soft masked genome

Question

[guillaume.rbt]

Hi all,

This is maybe a trivial question, but I can't find the answer anywere.

I'm working with the soft masked reference genome of Vitis vinifera : ftp://ftp.ensemblgenomes.org/pub/plants/release-38/fasta/vitis_vinifera/dna/Vitis_vinifera.IGGP_12x.dna_sm.toplevel.fa.gz

In this file I can find "N" and "n" characters (15.997.340 "n" and 433 "N)".

I guess they both represent gaps in the genome, but does anyone if there is a difference between lower and upper case "N" ?

(for info, in the unmasked genome there are 15997773 "N" and no "n")

Thanks,

Guillaume

[lieven.sterck]

There should not be any lowercase N (n), that makes no sense, cfr the answer of genomax . nothing you can do about it though it's just sloppy of the data provider

Answer 1

[GenoMax]

https://bioinformatics.stackexchange.com/questions/225/uppercase-vs-lowercase-letters-in-reference-genome

[guillaume.rbt]

thanks :) I missed that one

[Ram]

If you could add an excerpt, it would be a more complete answer.