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07-16-2011, 12:39 PM
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#1 |
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Junior Member
Location: Midwest, USA Join Date: May 2011
Posts: 5
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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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07-17-2011, 03:44 AM
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#2 |
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Senior Member
Location: USA, Midwest Join Date: May 2008
Posts: 1,178
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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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07-17-2011, 11:37 AM
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#3 |
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Junior Member
Location: Midwest, USA Join Date: May 2011
Posts: 5
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Thank you for your answer.
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07-18-2011, 06:50 AM
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#4 |
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Senior Member
Location: Bethesda MD Join Date: Oct 2009
Posts: 513
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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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07-18-2011, 07:27 AM
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#5 |
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Senior Member
Location: Bethesda MD Join Date: Oct 2009
Posts: 513
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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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07-19-2011, 03:41 AM
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#6 | |
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Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
Posts: 1,543
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Quote:
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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