fidelram
commented
6 years ago There are two ways to solve this. One is to set the maximum number of 'gene rows' to be plotted using gene rows = n, where n is the number of gene rows that want to be plotted. If a larger number of gene rows is needed, then only up to n rows are shown and some genes may be missing.
Other solution is to set global max row = yes, which will identify the maximum number of genes row needed given the .bed file and this number is always used.
depending on the number of genes in the selected genic region the gene annotation track is either clipped or the genes are displayed at very large scale. Would a dynamic scaling be possible (track height defined by number of overlapping genes).