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Old 11-02-2012, 09:42 AM   #1
meher
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Default Illumina base calling

Hi all,

Illumina genome analyzer Hiseq2000 produces the fastq files which has the phred quality scores. Could anyone give any explanation or reference to the phred algorithm used by Hiseq200 on how the probabilities are estimated to calculate the phred score?


Thanks in advance


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Meher
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Old 11-02-2012, 10:40 AM   #2
stinky
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I have the RTA theory of operations. It explains the scoring among other things....
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File Type: pdf RTA Theory of Operations v1.13.pdf (606.7 KB, 75 views)
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Old 11-02-2012, 11:29 AM   #3
meher
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Quote:
Originally Posted by stinky View Post
I have the RTA theory of operations. It explains the scoring among other things....
Hi,

Thanks for the response. The document refered by you gives the theoritical information, but i am interested in knowing the statistical model behind calculating probabilities?
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Old 11-02-2012, 01:21 PM   #4
stinky
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you might want to check these references. A bit older and address Sanger seq., but the models are still more or less the same.

http://genome.cshlp.org/content/8/3/175.long

http://genome.cshlp.org/content/8/3/186.long
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