so is this not true for mouse?
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Are lncRNA's present in the UCSC or ENSEMBL genome assemblies. My understanding is that the subset of poly-adenylated lncRNA's should be present in a TruSeq prep, and I am interested in aligning my reads to these.
Assuming human, yes. Ensembl include them in the annotation file "Homo_sapiens.GRCh37.68.gtf". UCSC has a special track for them called "lincRNAsTranscripts".
ENCODE annotated new data-set of lncRNA's (locus & transcripts) http://big.crg.cat/
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