Sat, 11/30/2013 at 11:12 AM
Customer asks for advice on how RNA-seq analysis may be analyzed for long ncRNAs.
Sat, 11/30/2013 at 11:50 AM
AccuraScience LB: Long ncRNAs can be assembled by mapping or by de novo assembly - depending on whether the reference genome is available - pretty much the same way as mRNAs. On the top of my head, some analyses you might need for your long ncRNA project include coding potential calculation (to confirm that they are actually non-coding RNAs), conservation analysis (long ncRNAs behave similarly to mRNAs for some conservation metrics, but differently for other conservation metrics, as defined by the two famous John Rinn's papers (one published in PNAS the other published in Nature Genetics in 2011). We could also check your ncRNAs against existing ncRNA datasets to see whether some of your ncRNAs have been reported before. And, if you would like, we could predict secondary structures of the ncRNAs - because those with predicted secondary structures are more likely to be functional.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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