Why do I get BED features outside the sequence when I'm loading a fasta file with fai index?


The most likely problem is that you accidentally loaded the fasta file AND the fasta.fai file. You do not have to load the index manually, GenomeView will treat is as a separate data source, hence the bed features popping up.

When you only load the fasta file, GenomeView will use the index for fast access, but you won't get the weird additional BED features.

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