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Old 03-28-2017, 12:35 PM   #1
kmcarr
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Default Realistic output for HiSeq 4000

The official spec for PF Clusters on the HiSeq 3000/4000 is 270-312M per lane. It seems that it is pretty easy to exceed this specification but I would like to ask regular operators of a 3000/4000 what PF cluster counts do you reliably get per lane? Is there a difference depending on library type?

Thanks.
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Old 03-28-2017, 01:49 PM   #2
misterc
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It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.
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Old 03-28-2017, 04:30 PM   #3
luc
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Quote:
Originally Posted by misterc View Post
It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.
Agreed. Long insert libraries (library molecules longer than 550 bp) will reduce yields and quality scores.
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Old 03-28-2017, 04:41 PM   #4
GenoMax
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Yield is not an issue as long as libraries have the right insert sizes. Illumina guidance is around 75% PF clusters for a good run.

There are optical duplicates but they appear to be randomly distributed when checked recently (n=1).
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Old 03-29-2017, 06:15 AM   #5
dpryan
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We usually get 300-400 million passing filter per lane on a HiSeq3000. "Optical" duplicates are typically below 10%, except with weird library types. Often the higher the read yield the lower the "optical duplicate" rate.
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