Difference between lower and upper case N in soft masked genome
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6.6 years ago
guillaume.rbt ★ 1.0k

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

genome masking reference • 1.7k views
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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

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thanks :) I missed that one

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

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