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Old 02-23-2010, 02:28 AM   #1
saima
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Default mismatches in maqView (why > 2)

i think that maq map command with n -2 determines that the maximum number of mismatches in alignment reads will be not greater than 2, but my output is showing a large number of mismatches (in red color) in a single read. why is this so?

can ruan jue or any one else reply

thanks
saima
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Old 02-23-2010, 06:15 AM   #2
lh3
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2 mismatches are guaranteed in the first 28bp. Occasionally you see 3. For whole reads, you may see even more mismatches.
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Old 02-23-2010, 06:51 AM   #3
saima
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thanks a lot.

i think you mean first 28 bps of every read but i am receiving mismatches in start of reads even.

i wish i could show u my output, if could be attached here.

Last edited by saima; 02-23-2010 at 06:54 AM.
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Old 02-23-2010, 07:18 AM   #4
saima
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Default to lh3(about mismatches in maqview)

Hi lh3,

here is my output attached (under attach files), you can see many mismatches even in first 28 bps of many reads.
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File Type: jpg Maq_view_mismatches.jpg (75.9 KB, 7 views)
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Old 03-23-2010, 08:10 AM   #5
Janet
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Question lots of mismatches in maqview

I am having the same problem but my mismatches are all shown in lowercase, therefore have lower Quality?
Can anyone explain this?
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