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  • Lower case characters in FASTa reference sequence

    Hi, I have noticed in HG19, there are sometimes a segment of sequence that are in lower case? Does this have a special meaning?

    Thanks

  • #2
    Often, sequence in loweracse is repetative. It's been soft masked so you can distinguish it from unique sequence

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    • #3
      What about those characters masked with "N", I thought those mean repeats too?

      BTW how does aligner like BWA take care "N"s, if it sees Ns in the reference does it automatically ignore those segment?

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      • #4
        Originally posted by foxyg View Post
        BTW how does aligner like BWA take care "N"s, if it sees Ns in the reference does it automatically ignore those segment?
        Hint: it is in the BWA paper.

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        • #5
          Can you kindly point out which paper it is please?

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          • #6
            Teach a human to fish...

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