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Old 09-08-2010, 07:52 AM   #1
foxyg
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Default 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
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Old 09-08-2010, 09:55 AM   #2
swbarnes2
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Often, sequence in loweracse is repetative. It's been soft masked so you can distinguish it from unique sequence
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Old 09-08-2010, 09:58 AM   #3
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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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Old 09-08-2010, 10:04 AM   #4
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Quote:
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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Old 09-08-2010, 10:15 AM   #5
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Can you kindly point out which paper it is please?
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Old 09-08-2010, 01:08 PM   #6
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Teach a human to fish...
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