quantifying ribosomal content in Illumina libraries
1 answer
Yes, you can use Picard CollectRnaseqmetrics.
I use these: https://github.com/dakl/genome
I've also seen people get them from the ucsc mysql dB. I guess they give very similar results.
You're right. In GRCh37, it maps to an unplaced contig. However, using these regions does distinguish between good and bad ribodepletions. With a good depletion, we get 0-2% rRNA content, and I our failed experiments with a robotic protocol with a bad sometimes see as high as 30%. With TruSeq Stranded Total RNA with Ribo-Zero Gold, we consistently get 0-2%.
But you are right, these values should be interpreted as relative within a series, rather than estimates of absolute rRNA content.
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