I am generating a pileup of BAM data from the 1000 genomes project using MPileup. I have associated the BAM file with the hg19 genome, but every single reference base in the output appears as an N. Is there some extra step I have to perform when using a BAM file that was not generated from within Galaxy?
Many thanks, luce ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
