Looking at custom BAM file with UCSC browser, I noticed that some reference genomic regions are not covered with reads. Does it mean that the regions have repeats and and the reads could not be placed unambiguously? Or is there another reason?
If your reads are not located in a particular genomic location, then either the reads really do not map there or you could try tuning the alignment tool's parameters. What reads are reported as mapped can vary between aligners.
Galaxy tutorials: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team