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?