Accurately identifying long non coding RNA from stranded total RNAseq(rRNA depleted)

Question

[m.sadman.sakib]

I have stranded Total RNaseq sequencing data(rRNA depleted) between two condition. Apart from gene level RNAseq analysis to find differential expression of genes, I am interested to look for non-coding RNA captured by total RNAseq. What could be the strategy for accurately mapping and quantifying for lncRNA/lincRNA? In short:

1.For example, for miRNA, there is mirDeep2 which is very useful to generate raw counts from the fastq files. But for lncRNA detection, is there any tool availble?

2.One could take the GTF file for long non coding RNA from GENCODE and rerun the whole analysis(indexing, mapping, counting). Will it be "comprehensive"?

I would really appreciate if someone experienced on working with long non coding RNA detection and quantification could comment on this aspect.

Thank you in advanced!