Hi, I have a "bed" format file containing model gene annotations from a plant genome and would like to convert this into a TranscriptDb object so that I can use EdgeR to count overlapping reads from an RNA-Seq experiment. Are there some tools available that can read the 'bed' file and produce a TranscriptDb object? I'm looking at the documentation on p. 6 in: http://bioconductor.org/packages/release/bioc/manuals/GenomicFeatures/ man/GenomicFeatures.pdf What is "exon rank?" Is this the order an exon appears in a transcript? If gene A is on the minus strand, is this the correct ranking of its exons, or does it matter? 1 2 3 <<<<<-----<<<<<<-----<<<<<< Does TranscriptDb assume 1-based or interbase coordinates? Very best wishes, Ann Loraine