I am studying Goldfish.it has not assembled and i use cuff links as we generated Reference genome of Goldfish. i can not find lncRNA by use cufflinks..it just have new isoforms no''u'"' class as mention in the literature that u, class is lncRNA and then i can analyze furher...but i can not find it in my data..i do not why
i use trinity. But i do not know next step....i have found some non-coding transcripts by using trinity. i have trinity.fasta file. i want to annotate lncRNA. How i can find it?? and how i can map to its reference Genome. and how i can use trinity.fasta file. for further analysis..now i have just find some non-coding RNA. i want to map it as my reference genome is not well assembled.so, how i can map it?