I am attempting to align my Illumina MiSeq paired end (2x250) reads to 2 different reference genomes in order to see which genes in the evolved samples are from which genome (phage recombination). I've used Bowtie2 and it appears to have worked since I get a BAM file. However when I try to use the Trackster visualization part I run into problems. I've created custom builds with the FASTA files of both phage genomes but when I try to add datasets to the visualization there are no options for me to select. Do I need to change the BAM files to a different format? Or is there some other way that would work better to visualize my alignment results? Any help or suggestions would be much appreciated!