Identification of non coding rna from transcriptome
How to identify non coding RNA like tRNA and 16S/18S rRNA from transcriptome data?
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Was the transcriptome data even created in a way to contain those sequences? The most common RNAseq library prep. method will largely exclude those.
Hi Devon,
Thank you for the response. You are right, it is not supposed to but I am just trying to see if there are any non coding RNA (by chance/ contamination?).
Any thoughts?
Try http://www.cbs.dtu.dk/services/RNAmmer/ for identifying the ribosmal RNAs. Also Transdecoder or coding potential calculator for identifying the non-coding transcripts.
My transcriptome assembly is quite but RNAmmer does not seem to accept more than 10,000 seqs.
From experience, the amount of rRNA in polyA-enriched library preps is on the order of 0.02%, which won't be usable. I presume tRNA is similar. You might pick up some of the non-coding polyA species though.