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Old 09-02-2010, 04:56 AM   #1
m_elena_bioinfo
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Default Different MAPPING QUALITY/PER-BASE QUALITY SCORE

Hi NGS users,
someone could explain me the different between MAPPING QUALITY and PER-BASE QUALITY SCORE?

The score for the pileup is the Phred score of mapping quality?

I have a bit of confusion about it!
Thanx a lot
ME
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Old 09-02-2010, 04:59 AM   #2
m_elena_bioinfo
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The mapping quality can be extracted from SAM or BAM file. But is there a way to do this using BIO:B::SAM modules?

To extract mapping quality using Bio:B::BAM, can I use:
$quality = $align->qual ?
It returns the quality score for the alignment as a whole.

Last edited by m_elena_bioinfo; 09-02-2010 at 05:53 AM.
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Old 09-02-2010, 09:00 AM   #3
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Quote:
Originally Posted by m_elena_bioinfo View Post
Hi NGS users,
someone could explain me the different between MAPPING QUALITY and PER-BASE QUALITY SCORE?

The score for the pileup is the Phred score of mapping quality?

I have a bit of confusion about it!
Thanx a lot
ME
Read the supplementary materials in the Li et al. MAQ paper (Genome Research).
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