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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
Thank you,
Vedbar
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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. -
Thank you for your answer.Comment
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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.
HaroldComment
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Follow-up:
The bam files contain Phred+33 Q-scores, while the export files contain Phred+64.
Aaaarrgghh!Comment
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See new post on the earlier thread, http://seqanswers.com/forums/showpos...9&postcount=64Originally posted by HESmith View Post
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=8895Comment
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