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Old 07-18-2012, 11:28 PM   #1
kaixinsjtu
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Exclamation A question about the MAPQ (mapping quality) in SAM file

hey everyone,

I am looking into a SAM file now and found the MAPQ field all filled with 255. 255 means mapping quality not available, right? So I want to use bowtie to remap the tags in Fastq format, and hopefully get the mapping quality scores instead of 255.

My question is, with bowtie, how to calculate the MAPQ for each tag? I have read the bowtie manual and got no clue at all... If I use "--MAPQ <int>", that means I set the quality by myself. But I don't know it. Shouldn't bowtie be able to calculate quality scores for each tag based on the fastq file??

Thanks for your help in advance!
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Old 07-19-2012, 12:59 AM   #2
pole_sana
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Default Peak calling for TSS detection

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Last edited by pole_sana; 07-19-2012 at 01:10 AM. Reason: wrong thread
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Old 07-20-2012, 01:07 AM   #3
Bukowski
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Quote:
Originally Posted by kaixinsjtu View Post
hey everyone,

I am looking into a SAM file now and found the MAPQ field all filled with 255. 255 means mapping quality not available, right? So I want to use bowtie to remap the tags in Fastq format, and hopefully get the mapping quality scores instead of 255.

My question is, with bowtie, how to calculate the MAPQ for each tag? I have read the bowtie manual and got no clue at all... If I use "--MAPQ <int>", that means I set the quality by myself. But I don't know it. Shouldn't bowtie be able to calculate quality scores for each tag based on the fastq file??

Thanks for your help in advance!
Despite what it says in the SAM spec, I think for Bowtie this just means "alignment is non-repetitive" if you're using the default parameters.
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Old 07-20-2012, 06:24 AM   #4
kaixinsjtu
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Originally Posted by Bukowski View Post
Despite what it says in the SAM spec, I think for Bowtie this just means "alignment is non-repetitive" if you're using the default parameters.
Thanks! But where is the mapping quality in SAM file? I want to calculate the probability that the tag is mapped incorrectly.

Thanks again.
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Old 07-20-2012, 06:26 AM   #5
Bukowski
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If you're looking for MAQ stype mapping qualities I don't think it does them, but I'm happy to be proven otherwise.
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Old 07-20-2012, 06:49 AM   #6
kaixinsjtu
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If you're looking for MAQ stype mapping qualities I don't think it does them, but I'm happy to be proven otherwise.
Thanks! I will look into MAQ
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Old 07-20-2012, 06:50 AM   #7
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Thanks! I will look into MAQ
If you're going to take that step back, look at BWA instead which largely supercedes MAQ and still has sensible mapping qualities generated for variant calling.
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Old 07-21-2012, 12:35 AM   #8
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If you're going to take that step back, look at BWA instead which largely supercedes MAQ and still has sensible mapping qualities generated for variant calling.
Thanks!!
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