how can I get long non coding RNA from RNA-seq data

Question

[hodatn]

Hello friends. Does anybody know how can I get long non-coding RNA from RNA-seq data? The genome of the organism is not available. I want to detect lncoding RNAs and analyze them.

[lieven.sterck]

short answer?: Filter out everything that is protein coding and the remainder is (long) non-coding .

For more elaborate answer(s) you might need to provide some more info, such as: what is the goal, what kind of data you have at hand, genome availability , ....

Answer 1

[i.sudbery]

There are many reviews on this subject of find lncRNAs.

Try this one and this one for starters.

Both of these concentrate on species where the genome is available, but have some useful tips if you are looking to put together a protocol for doing in an unannotated genome.

I guess you'd start by doing a denovo transcript assembly with something like Trinity. Then Blast against transcriptomes from other species, removing matches to protein coding genes. Then assess the coding potential of the transcript using one of the coding potential predictors mention in the above reviews.

There are probably pipelines already build for for this stuff, but I don't know them (well other than the Ensembl pipeline, but I'm guessing you don't want to be running that!).