How can I import a genome into IGV with annotations?
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5 weeks ago
dxm958 • 0

I want to import a genome from a FASTA file into IGV and include annotations. I have tried to import the contig and scaffold FASTA files but this doesn't seem to work. I imagine I need the assembled genome but I have no idea where to start - please help!

Genome: https://data.nal.usda.gov/dataset/drosophila-biarmipes-genome-assembly-dbia-20

Annotations: https://data.nal.usda.gov/dataset/drosophila-biarmipes-genome-annotations-v053-genome-assembly-dbia20

Thanks!

IGV • 101 views
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5 weeks ago
GenoMax 110k

You don't need an assembled genome but the identifiers between the reference and annotation file need to match. Use a multi-fasta sequence file for reference and then a GTF/GFF file for annotations.

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

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