mismatches in maqView (why > 2)

saima · 02-23-2010, 02:28 AM

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

lh3 · 02-23-2010, 06:15 AM

2 mismatches are guaranteed in the first 28bp. Occasionally you see 3. For whole reads, you may see even more mismatches.

saima · 02-23-2010, 06:51 AM

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.

saima · 02-23-2010, 07:18 AM

Hi lh3,

here is my output attached (under attach files), you can see many mismatches even in first 28 bps of many reads.

Janet · 03-23-2010, 08:10 AM

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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02-23-2010, 02:28 AM	#1
saima Member Location: sweden Join Date: Feb 2010 Posts: 15	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

02-23-2010, 06:51 AM	#3
saima Member Location: sweden Join Date: Feb 2010 Posts: 15	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.

03-23-2010, 08:10 AM	#5
Janet Junior Member Location: Norwich Join Date: Nov 2009 Posts: 1	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?

02-23-2010, 06:15 AM	#2
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	2 mismatches are guaranteed in the first 28bp. Occasionally you see 3. For whole reads, you may see even more mismatches.