Hello. I'm working on a project to examine gene expression in a system where RNA-processing has gone awry. I expect to see aberrant splicing, alternative transcription start site usage, aberrant poly-adenylation and capping, etc. RNA-seq is the perfect tool for looking at both differential expression and strange RNA-structural events.
But I don't want to do a poly-A selection because I'll probably lose all these odd transcripts that I'm most interested in that might not be properly polyadenylated, spliced, capped, etc. Yet I don't want to sequence a ton of rRNAs and tRNAs.
What kind of library preparation techniques should I investigate that don't require a poly-A selection?
Many thanks.
But I don't want to do a poly-A selection because I'll probably lose all these odd transcripts that I'm most interested in that might not be properly polyadenylated, spliced, capped, etc. Yet I don't want to sequence a ton of rRNAs and tRNAs.
What kind of library preparation techniques should I investigate that don't require a poly-A selection?
Many thanks.
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