I've done a tophat2 mapping of human RNA-seq expts in usegalaxy.org. After getting the accepted hits bam files, and downloading both bam and bai files, I cannot visualize the mapped reads track in my local IGV. Remote visualization in main UCSC is OK.
I also tried sorting in Galaxy the bam files, downloading both bam and bai, but still don't work in local IGV.
Any help would be very much appreciated.