For those of you contemplating Rna-seq experiments, here is a tip:
consider methods to deplete ribosomal RNA before sequencing.
In aphid rna-seq data now at NCBI/SRA, the rRNA genes (spread over a
mere 300 Kb of poorly assembled scaffolds) account for 50% to over
90% of rnaseq reads, depending on experiment and body tissue. These
clog up analyses as well as waste useful experimental effort
(i.e. for 1.1 billion aphid reads available, 900 mill are rRNA reads,
with 200 million for the rest of transcriptome).
I have no experience in the methods involved, but here are examples
-- Don Gilbert
RNA-Seq quantitative measurement of expression through massively parallel RNA-sequencing
"2.2. rRNA removal
One of the principal technical hurdles to overcome with RNA-seq is the fact that
the vast majority of RNA (>90%) present in cells consists of ribosomal RNA (rRNA)."
"Ribosomal RNA depletion ..
Ae. aegypti .. subjected to eukaryotic ribosomal RNA depletion using the RiboMinus Kit (Invitrogen) "