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
For gene annotation, you may want to try Apollo: a sequence annotation editor. If I remember it correctly, you will need your genomic sequence (does your species have an assembly? What is your species btw?) and mRNA/ESTs files to map to the genome and call the gene models (coding and otherwise). Check the Apollo User Guide for more details. There could be loads of things you could use your files for, it depends on the question you are trying to answer. Have a look at the 'Post Transcriptome Assembly Downstream Analyses' from the Trinity GitHub. They seem to give more ideas on annotation in their Genome Annotation Using Trinity and PASA page.
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. i use trinity. But i do not know next step.