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

Join Date: Aug 2011
Posts: 239
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Quote:
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.

Quote:
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.


Quote:
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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