Is there a way to import a large amount of regions of interest into IGV

Question

[Mark]

This is my scenario.

I have a reference genome and aligned sequencing reads imported into IGV. I also have a separate fasta file that contains the sequence of around 1000 marker genes taken from the reference genome. What I ideally like to do is figure out on which chromosomes and which loci those marker genes are located, have those regions automatically annotated as regions of interest, and then quickly browse through all 1000 loci to see how the sequencing alignment looks in those locations. I'm not very familiar with using IGV yet so if anyone has any recommendations on how to do this that would be very appreciated.

[ATpoint]

Which genome are we talking about? Something common like human or mouse for which GTF annotations exist? IGV can read BED files for example, so making a table chr-start-end-name would be easy.

[GenoMax]

I also have a separate fasta file that contains the sequence of around 1000 marker genes taken from the reference genome. What I ideally like to do is figure out on which chromosomes and which loci those marker genes are located

You need to have the location information available in addition to the sequence. IGV on its own can't figure this part out. As @ATPoint noted you will need to provide that information as a BED file (may be the easiest to do).