did u try CummeRbund? http://compbio.mit.edu/cummeRbund/ best, ib -- View this message in context: http://r.789695.n4.nabble.com/Comparing-two-gff-gtf-files-de-novo-transcripts-v-s-reference-tp3934629p4639032.html Sent from the R help mailing list archive at Nabble.com.