FP Value?
What does the "FP value" mean showed in the Illumina HiSeq sequencing data report?
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What does the "FP value" mean showed in the Illumina HiSeq sequencing data report?
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Does anyone know anything about this? I only know that FP value is a percentage number. -
maybe False Positive rate. check did you search documentation files?Comment
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But the FP value is the higher the better. So I don't think it's false positive.
And the illumina man did not know how to calculate, but say it is a evaluation indicator.Comment
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Do you mean PF?? PF==Passed Filter. It is expressed a %. The values should be in the 85-90% range.Originally posted by wangxin View Post What does the "FP value" mean showed in the Illumina HiSeq sequencing data report?Comment
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Yes, thank you for your answer. I think it is PF I'm looking for. One more question is that do you know something more about PF, like how to calculate, what does it represent? Thanks!Originally posted by kmcarr View PostComment
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By default the Illumina software uses what it calls the "Chastity" filter. From Illumina documentation:Originally posted by wangxin View Post
As you can see from the description the software only considers the first 25 cycles of read 1 in determining whether a read passes filtering. This means that from cycle 26 on the quality can go to hell in a handbasket and the read will still pass. You must further QC filter your reads before downstream analysis.The chastity of a base call is the ratio of the intensity of the greatest signal divided by the sum of the two greatest signals. Reads do not pass the quality filter if there are two or more base calls with chastity of less than 0.6 in the first 25 cycles.Comment
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Thanks a lot, Kmcarr. It's very clear.Comment
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