Hi folks,
I have several human RNA-Seq datasets (libraries prepared from total RNA using the TruSeq Stranded Total RNA kit from Illumina) that I would like to search for lnc-RNAs (both known and unknown).
Is this possible? I read that some library prep kits do not keep all lnc in - but this kit does not do poly-A enrichment, so it should be ok?
Known lnc should not be a problem with normal alignment procedures. How would you suggest to hunt for novel lnc-RNAs?
Cheers!
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aggregatibacter
It's a total RNA kit, so it should be fine for lncRNAs. GENCODE has many lncRNAs annotated. You also should look into MiTranscriptome (large-scale ab initio transcriptome meta-assembly from 6,503 RNA-Seq libraries): http://mitranscriptome.org/
Hunting for novel lncRNAs is not trivial. They are not highly expressed, so it's hard to distinguish the signal from the noise. If you identify a potential novel transcript, you need to determine if it's a lncRNA using metrics like size, coding potential, and nearby genes. lncRNA blog keeps a reasonable log of available tools:
Thanks for pointing me to the mitranscriptome, I had not seen that project before...
Checkout this review: Predicting long non-coding RNAs using RNA sequencing.
In a nutshell, you are going to want to apply a transcript assembly algorithm like cufflinks or stringtie (I just tried out stringtie, and it ran in 40 minutes where as cufflinks took 50 hours, so I recommend that), and then filter like crazy.
Many thanks for the quick and helpful advice..
What kinds of "crazy" filters do you have in mind?
PS: The link is broken.
What kinds of "crazy" filters do you have in mind?
PS: The link is broken.
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