4.6 years ago by
It is useful to know what fraction of your reads are rRNA as a basic quality metric, but if you did poly A selection (vs a ribosomal depletion method e.g. ribo zero) it's probably low and if you have enough other reads from your plant to get what you want out of it you could get away with not knowing the exact rate. The only reason people care about it as a metric is that high rRNA wastes reads.
That said, you could align your reads to whatever rRNA you have from the closest plant. Usually the rRNA is quite conserved so if you use lax alignment parameters you'll get a ballpark estimate of whether you have a problem or not.
Also, I would imagine you will be assembling your transcriptome. If you throw it through Trinity the rRNA should assemble like any other transcripts so you'll have the real rRNA sequences at the end. Then you can align back to the sequences and see what you have.
You do want to know your rRNA rate before you sequence more libraries in case your protocol needs tweaking.