lncRNA and circular RNA identification softwares

Question

[Rituriya]

Hi All,

I have total RNA-seq data from Illumina. I am trying to find a decent software to detect and analyse long non-coding RNA (lncRNA) and circular RNA (circRNA).

For circRNA, I am thinking of circExplorer2 mostly. Please suggest any other alternatives. I am unable to find a software for lncRNA analysis. Please help as I am new to this kind of data.

Thank you, Rituriya.

[piyushjo]

Any annotation, whether RefSeq or GENCODE already includes bunch of lncRNAs. You can use biomaRt package to figure out which of the gene id's belong to lncRNA class.

If you looking for novel lncRNAs, those that are not annotated yet, there are bunch of papers you can follow.

https://www.nature.com/articles/s41598-017-14595-3

https://www.ncbi.nlm.nih.gov/pubmed/30055874

In my analysis, I used Lncipedia annotation. As the database is composition of various predicted annotated lncRNA trasncripts, its a good starting point, unless you really want de novo prediction.

Also read the below paper for more idea about lncRNA detection from RNA-seq.

https://www.ncbi.nlm.nih.gov/pubmed/31243368

Hope it help!

[Rituriya]

Thank you piyushjo for the directions. I will definitely go through the articles suggested.

Answer 1

[Rituriya]

For lncRNA only, if it helps anyone, I am planning to try out softwares discussed in following thread: Currently what is the best tool for long non-coding RNA annotation? Is FEELnc a strong contender?