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Old 02-01-2012, 11:19 AM   #3
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Location: Brazil

Join Date: Jul 2010
Posts: 6

Originally Posted by Melissa View Post
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.
Hi Mellissa
I have a worse situation than Nigel. My sequencing results showed 86% of rRNA ( I have to check the parameters used). The service provider showed me the mRNA agilent profile and it indicated 11% of rRNA contamination (poly A purification). How did it become 86%? What percentage of ribosomal RNA contamination is acceptable in the purified mRNA for 454 sequencing?
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