IGV, reference genome problem

Zohreh Fazelan

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Nov 26, 2024, 9:08:03 AM11/26/24

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Could you please guide me? I use the reference genome of American lobster. I uncompressed the file and it is an uncompressed.fasta.fai file, but it is not opened through IGV. How should I fix it?

Zohreh Fazelan

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Nov 26, 2024, 4:24:34 PM11/26/24

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Hi,

Is there nobody to guide me??

igv-help

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Nov 26, 2024, 4:32:45 PM11/26/24

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The .fai file is the index file that goes with the main .fasta file. You need to load the .fasta file. If you are using the IGV desktop application, make sure the .fasta and .fai files are in the same folder, then load the .fasta file via Genome > Load Genome from File.

Zohreh Fazelan

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Nov 26, 2024, 8:40:31 PM11/26/24

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Thanks for your response. The .fasta and .fai files are in the same folder and I loaded .fasta file. I also loaded the HISAT file and StringTie merge file. In the attached photo, I can not see the genome. Is it normal or did I make a mistake?

I also attached a photo of loaded files, showing their types. Thanks for your help!

Untitled01.png

Zohreh Fazelan

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Nov 26, 2024, 8:48:42 PM11/26/24

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I use IGV_2.18.4, Windows 10.

igv-help

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Nov 27, 2024, 12:01:40 PM11/27/24

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Are you loading the fasta from the Genomes menu?

igv-help

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Nov 27, 2024, 2:00:33 PM11/27/24

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Your screenshot looks normal, I'm not sure what the problem is, what do you expect to see?

Also, I don't know what a "HISAT" or "StringTie" merge file is, how were they loaded?

Zohreh Fazelan

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Nov 28, 2024, 6:33:13 PM11/28/24

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Thank you so much. You are right. I did it correctly. Thanks!

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