custom HIV-1 ref. genome

[DOrso lab]

We want to create a modified HIV-1 reference genome (different to the one listed in IGV: gi|9629357|ref|NC_001802.1) because HIV-1 isolates have different sequences and we need this one for mapping purposes. Would it be possible to obtain the fasta file used for the creation of this genome to use as example, in addition to a description of what else is needed? Thanks! Ivan-

[James Robinson]

The only thing needed is the fasta file itself, which of course you would need to provide.   To define your reference, simply load the fasta file from the "Genome" menu (note, not the "Files" menu).   The first time you load it an index file will be created if it doesn't already exist.   After the reference (fasta) is loaded you can load any annotations you have fro the "Files" menu.

[DOrso lab]

Thanks for the reply. Can you share the pasta file used to create the current HIV-1 genome listed in IGV so we can use it as a reference since we need to build this file from scratch, it seems. Thanks in advance! Ivan-

[James Robinson]

I don't understand how this will help you but the fasta is here https://s3.amazonaws.com/igv.org.genomes/covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna

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