Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file

I find that in hg19 fasta file, the sequence contains capital letters(ATGC) and lowercase letters(atgc), so I am wondering is there any difference between these 2 kinds of letters, or is there any special meanings?

fasta hg19

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updated 12.3 years ago by Pierre Lindenbaum

• written 12.3 years ago by Chen Sun

1 answer

See http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/

Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.

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updated 6.6 years ago by Ram

• written 12.3 years ago by Pierre Lindenbaum

I'll add that the term for this is "soft masking" (as opposed to "hard masking", wherein these bases would simply be replaced by Ns).

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written 12.3 years ago by Devon Ryan

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