I mapped my peak using MACS in Galaxy using the built-in genome. I can visualize my peaks in IGB via Galaxy but the reference genome is not annotated. If I select my species (E. coli) in IGB, then my peaks (tracks) disappear from the window and data management table. It is the same if I open IGB first, load my reference genome via quickload before viewing my galaxy data. It seems I can't have both.
As soon as I load my bed file, I have the coordinates, but no nucleotide sequence. I could manually load my UCSC genome, but then the genes have codes, not names.
Any help would be much appreciated !