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Old 07-16-2011, 12:39 PM   #1
vedbar
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Default Quality Score Format

Is there any difference in the quality score format of a sample (FASTQ) file generated by HiSeq 2000 and that by Genome Analyzer II ?


Thank you,
Vedbar
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Old 07-17-2011, 03:44 AM   #2
kmcarr
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There are no differences between machines, but there are between software versions. The recently released CASAVA 1.8 outputs FASTQ files with Q-scores using Phred+33 encoding as opposed to the Phred+64 used in previous versions.
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Old 07-17-2011, 11:37 AM   #3
vedbar
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Thank you for your answer.
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Old 07-18-2011, 06:50 AM   #4
HESmith
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Hi kmcarr,

I know that CASAVA v1.8 is reported to produce Phred+33 Q-scores, but I just checked the export files from our last run and observed quality values up to 'i' (which would be 72!). I'll contact Illumina tech support later today and get the scoop.

Harold
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Old 07-18-2011, 07:27 AM   #5
HESmith
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Follow-up:

The bam files contain Phred+33 Q-scores, while the export files contain Phred+64.

Aaaarrgghh!
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Old 07-19-2011, 03:41 AM   #6
maubp
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Quote:
Originally Posted by HESmith View Post
Follow-up:

The bam files contain Phred+33 Q-scores, while the export files contain Phred+64.

Aaaarrgghh!
See new post on the earlier thread, http://seqanswers.com/forums/showpos...9&postcount=64

It sounds like they've fixed their FASTQ (good), but not the in house "export" format (confusing!)

SAM/BAM have always explicitly required PHRED scores + 33 for the ASCI encoding (like Sanger FASTQ).

Probably best to continue this here: http://seqanswers.com/forums/showthread.php?t=8895

Last edited by maubp; 07-19-2011 at 03:46 AM. Reason: typo
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