A question about the MAPQ (mapping quality) in SAM file

kaixinsjtu · 07-18-2012, 11:28 PM

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!

pole_sana · 07-19-2012, 12:59 AM

...........

Bukowski · 07-20-2012, 01:07 AM

Quote:

Originally Posted by kaixinsjtu

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.

kaixinsjtu · 07-20-2012, 06:24 AM

Quote:

Originally Posted by Bukowski

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.

Bukowski · 07-20-2012, 06:26 AM

If you're looking for MAQ stype mapping qualities I don't think it does them, but I'm happy to be proven otherwise.

kaixinsjtu · 07-20-2012, 06:49 AM

Quote:

Originally Posted by Bukowski

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

Bukowski · 07-20-2012, 06:50 AM

Quote:

Originally Posted by kaixinsjtu

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.

kaixinsjtu · 07-21-2012, 12:35 AM

Quote:

Originally Posted by Bukowski

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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07-18-2012, 11:28 PM	#1
kaixinsjtu Junior Member Location: HOUSTON Join Date: Nov 2008 Posts: 9	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!

07-19-2012, 12:59 AM	#2
pole_sana Junior Member Location: south of one of the poles Join Date: Jul 2012 Posts: 6	Peak calling for TSS detection ........... Last edited by pole_sana; 07-19-2012 at 01:10 AM. Reason: wrong thread

07-20-2012, 06:26 AM	#5
Bukowski Senior Member Location: UK Join Date: Jan 2010 Posts: 390	If you're looking for MAQ stype mapping qualities I don't think it does them, but I'm happy to be proven otherwise.