I use IGV to view BAM files. Most times I'm viewing single chromosome genomes. When view single chromosomes I'm able to view annotations by making a .genome using a fasta and gff file. However on occasions I need to view 2 chromosomes in a single BAM. These BAM files have been made using a reference genome where the 2 fasta files have been concatenated into a single file. I've tried making a .genome in IGV with concatenated fasta and gff files, but the annotations for the first chromosome does not show for the first 100,000 bases. Fasta and gff files being used are ref_seq, so the formatting of theses files should be correct.
Something is wrong with how I'm inputting the annotated files. Is there a proper way of showing annotations for multiple chromosomes in IGV?