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Old 09-13-2018, 05:57 AM   #1
R0bert
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Default bcl2fastq2 html output column meanings

Hi,

I have a question concerning the bcl2fastq2 html output. I'm attaching an example lane summary table found in the html output.
I'm wondering what the meaning of the "% PF Clusters" column (7th column) is. Is there another pass filter applied than the one resulting in the PF Clusters (2nd column)?

Thanks and best,
Robert
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Old 09-14-2018, 05:11 AM   #2
kmcarr
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Quote:
Originally Posted by R0bert View Post
Hi,

I have a question concerning the bcl2fastq2 html output. I'm attaching an example lane summary table found in the html output.
I'm wondering what the meaning of the "% PF Clusters" column (7th column) is. Is there another pass filter applied than the one resulting in the PF Clusters (2nd column)?

Thanks and best,
Robert
Robert,

No, there is no additional filtering. The %PF column is telling you what percentage of the original (Raw) clusters those reported PF clusters represent. You could back calculate from the data given how many Raw clusters there were (see table).

As an aside 15% PF is very poor for any Illumina instrument and the reported quality is very poor as well. You should discuss these issues with whomever performed the sequencing run.
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