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Old 04-26-2011, 07:39 PM   #2
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Location: Switzerland

Join Date: Aug 2008
Posts: 124

I think this topic has been discussed in the old thread. Back in the days when people are still using Invitrogen Ribominus kit, 30-40% rRNA in a RNA-Seq data is quite good. The new kits should perform better. In my own experience, percentage of rRNA in the data depends very much on the mapping parameters you use. I can map 30% if I allow 2 mismatch in 50bp reads but up to 50% if I use a min of 30bp extract matching. That's a huge difference.
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