Question: Detection of (novel) lnc-RNAs in 'normal' RNA-Seq data
0
gravatar for aggregatibacter
2.8 years ago by
Bonn, Germany
aggregatibacter110 wrote:

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!

long non-coding rna rna-seq • 1.2k views
ADD COMMENTlink modified 2.6 years ago by Friederike4.2k • written 2.8 years ago by aggregatibacter110
2
gravatar for igor
2.8 years ago by
igor7.6k
United States
igor7.6k wrote:

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:

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by igor7.6k

Thanks for pointing me to the mitranscriptome, I had not seen that project before...

ADD REPLYlink written 2.8 years ago by aggregatibacter110

It seems really promising. Not sure why it's not more widely known.

ADD REPLYlink written 2.8 years ago by igor7.6k
0
gravatar for i.sudbery
2.8 years ago by
i.sudbery4.5k
Sheffield, UK
i.sudbery4.5k wrote:

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.

ADD COMMENTlink written 2.8 years ago by i.sudbery4.5k

Many thanks for the quick and helpful advice..

ADD REPLYlink written 2.8 years ago by aggregatibacter110

What kinds of "crazy" filters do you have in mind?

PS: The link is broken.

ADD REPLYlink written 2.6 years ago by Friederike4.2k

Some options: length, expression level, coding potential

ADD REPLYlink written 2.6 years ago by igor7.6k
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