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Old 04-19-2011, 03:02 AM   #1
Nigel Saunders
Junior Member
Location: UK

Join Date: Apr 2011
Posts: 1
Default How much rRNA sequence is reasonable in an RNA-seq dataset?

Dear all,
I have just received two RNA-seq datasets from a bacterial comparision. The reads are at least 50% (have not been able to look deeper yet) of 16 and 23S rRNA (i.e. all the top over-represented sequences by fastqc are rRNA). The centre that processed this insisted on doing the RNA depletion as part of their pipeline, and I believe used the Ribo-Zero (Epicentre) methodology which is supposed to be a good one.
What percentage post depletion should I have typically expected? Is this normal, or have they failed to do the rRNA depletion properly?
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