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09-08-2010, 08:52 AM
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#1 |
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Member
Location: US Join Date: May 2010
Posts: 54
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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 |
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09-08-2010, 10:55 AM
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#2 |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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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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09-08-2010, 10:58 AM
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#3 |
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Member
Location: US Join Date: May 2010
Posts: 54
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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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09-08-2010, 11:04 AM
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#4 | |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Quote:
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09-08-2010, 11:15 AM
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#5 |
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Member
Location: US Join Date: May 2010
Posts: 54
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Can you kindly point out which paper it is please?
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09-08-2010, 02:08 PM
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#6 |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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