Thanks for your previous help. I use these demonstration files https://zenodo.org/record/582600#.WczAmkojFhA uploaded them as fastqsanger and run bwa-mem with NC_007795.1 reference after NormalizeFasta. I got a BAM file.
I would like to view the BAM on IGV locally but can not. I have igv locally and open it first then click the link for "display with IGV local" but files appear empty even if I zoom to 100bp. I also download the galaxy bam/bam.bai files from Galaxy and upload to igv independently. it also seems empty.
I would appreciate your help. thanks!