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Old 04-21-2015, 05:49 AM   #2
Location: Germany/Netherlands

Join Date: Feb 2014
Posts: 98

No clue what the biological cause could be.
What are your genes in this case? Protein coding sequences, or also noncoding RNA? If noncoding is included, does it also include noncoding besides tRNA and rRNA?
I ask because the rRNA read removal (under the assumption you don't do that by mapping do your reference, but with e.g. sortMeRNA) is not fully reliable (depending on how close your organism to anything in the database is), and you might still end up with a half ton of rRNA/tRNA. And if that's not the case, also tmRNA might have a very high expression value.

And what does the fastQC report say?
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