Is there anything with a poly-A tail that isn't included in Ensembl's cDNA reference?
Like lncRNA's or pre-mRNA's that have a polyA tail but still have introns?
Thanks
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ericbrenner •
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The answer is: probably. But what are you looking for ? Or more precisely, where do you want to look for these things ? Are you interested in a species in particular ? Are you interested in cDNAs that have been already annotated or in raw sequences ?
I was thinking things like lncRNA's or miRNA intermediates that haven't finished being processed. I've since learned that miRNA's are not included. Not sure about the rest. Basically, if I have raw RNA-seq data (corresponding to everything with a polyA tail), what reference(s) should I use for annotation if I want to make sure I don't leave out anything. I think annotating using the Ensemble cDNA reference and then using the Ensemble ncRNA reference should cover everything. I could also use a genome reference, but that wouldn't work with the speedy programs like Kallisto :/
I would think that mapping your reads to the Ensembl transcriptome would take care of this. Ensembl annotates all sorts of non-coding RNAs including miRNAs.