How to load genome on IGV?
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6 weeks ago
Joe • 0

I'm new to IGV and I'm trying to load my own genome but it just isn't working. This is the genome I'm interested in:

https://www.ncbi.nlm.nih.gov/genome/5296?genome_assembly_id=700425

On the graphical viewer I've clicked "Download", then downloaded the FASTA of the whole thing. The file is called "GU305914.1[1..230408].fa" The IGV website says that I can load my own genome if I have the FASTA file:

https://software.broadinstitute.org/software/igv/LoadGenome

I tried this on the IGV web browser (https://igv.org/app/), and I get this error message:

"Genome did not load - invalid data and/or index"

I also tried loading from URL by entering the ncbi url above, which also didn't work. How do I load the genome onto IGV?

Thanks in advance

IGV • 220 views
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6 weeks ago
GenoMax 109k

Did you click "Send to" and then select "File" from this page? If you do that then that should save it as a plain text fasta file. I suggest that you download the IGV local app for your OS and then follow the directions you linked above for LoadGenome. Necessary index for the fasta file is automatically created in that case.

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The file wouldn't work on the web app but did work on the local IGV, thanks!

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