long noncoding RNA DE analysis

[frymor]

Hi everybody,

I am looking for a method/tool/workflow to analyse the differential expression of long ncRNA in C. elegans.
After searching the web for quite some time, I can't find a complete method to do so. Some people recommend to just run the "usual" DE analysis using tools like DESeq2/edgeR and than look for the lncRNA transcripts in the results.

But this doesn't seems to work well. I also not sure, if this is the correct way. I have find some tools specifically for the analysis of lncRNA expression (e.g. CNCI, UlncR, ...), but none of them is working either completely or for C. elegans specifically.

I was wondering if anyone know a tool/method for analysing differential expression of long non-coding RNAs in C. elegans or can point me to a functioning workflow.
Maybe an explanation of how to do so is what I need.

I would appreciate any help I can get.

Thanks
Assa

[Arkajyoti Banerjee]

I think lncDIFF is one good package in R that is specifically designed for lncRNA DE analysis. I myself am trying to work on DE analysis of non coding RNAs currently.