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Old 05-02-2016, 05:06 AM   #13
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239

Originally Posted by GenoMax View Post
@Jane_M: Apologize for the posts from last week. I must have missed them. They were indeed waiting for moderation.
Thank you for posting them.

Originally Posted by GenoMax View Post
Thank you for providing detailed stats. It does appear that the ribo-depletion did not work well. Someone with experimental expertise can comment but % of rRNA should be less than 5% (perhaps 1% or less is ideal).
I had the impression that 5% was already a good ribodepletion ratio. Let's see if others can give their feedback.

Originally Posted by GenoMax View Post
Interestingly (if I am reading this right) most of your duplicates (>98%) on the 4000 are optical, with a lesser % in regular run.
Well, on HiSeq 4000, more than 99% of the READ_PAIR_DUPLICATES are READ_PAIR_OPTICAL_DUPLICATES. This ratio reaches 88% for NextSeq 500. Are there optical duplicates too? If not, what are they?

Can someone please comment these two ratio: 35% (on ribodepleted sample - HiSeq 4000) and 51% (on polyA sample - NextSeq 500) for PERCENT_DUPLICATION?

Last edited by Jane M; 05-02-2016 at 05:10 AM.
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