When trying to view Galaxy generated BAM files (from MACS and/or Star) in IGB, it seems that the database/build associated with the BAM files (hg19 with mtDNA replaced with rCRS) is not recognized by IGB, so the BAM files load in to IGB showing custom genome as oppose to the one identified in Galaxy. I have tried all of the available options in Galaxy to see if any would work but none have been successful. From what I can gather IGB uses UCSC genomes but I am not sure about Galaxy. That seems to leave only two options:
1) Retrieve the fasta file for the Galaxy hg19 genome and use that to create a genome in IGB. However, I have been unable to determine the location of the references.
2) Upload the UCSC genome reference to Galaxy and use that for alignment and MACS, so that I can then visualize in IGB.
Any guidance to solve this issue would be greatly appreciated. Thanks!!