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-   -   Realistic output for HiSeq 4000 (http://seqanswers.com/forums/showthread.php?t=75081)

kmcarr 03-28-2017 12:35 PM

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.

misterc 03-28-2017 01:49 PM

It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.

luc 03-28-2017 04:30 PM

Quote:

Originally Posted by misterc (Post 205725)
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.

GenoMax 03-28-2017 04:41 PM

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).

dpryan 03-29-2017 06:15 AM

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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