I have been using Galaxy Main to map WGS data from E. coli. I have tried several mapping approaches against the eschColi_K12 reference and I think the sequencing data is mapping correctly (From bam.iobio.io: >99% mapped reads, >95% proper pairs, >40 mapping quality score). However, when I try to view the data in either IGV or IGB, these programs are not locating the eschColi_K12 genome and no sequencing data is showing up. Is there a step I am missing to be able to view my data against the reference? I have made sure the data is sorted and indexed and it hasn't changed the results.
Any help or suggestions will be greatly appreciated.