I have a question about using cufflinks for transcriptome assembly. Once we generate a new gene model/transcriptome for a specie what are the various ways in which one could compare the cufflinks generated transcript model to an already existing one in the UCSC genome browser or for that matter predicted computationally.
I have the existing gene model in gff3 format and cufflinks generate the output in gtf format. Any tool that could compare these files. May be I could use bedtools but then I need to convert my gtf file into bed or gff3
I am trying to better understand how can we use the real RNA-Seq data to find differences with the known annotation model and improve it further.
Any references would help too.