Create custom JSON File

[Luigi Marongiu]

Hello,

I am new to the use of IGV. I would like to create a custom genome annotation for E. coli NZ_CP097881.. What would be the procedure?

Thank you

[igv-help]

We're in the process of updating our User Guide, but in the meantime you can find the documentation describing IGV's .json genome format here: https://github.com/igvteam/igv/wiki/JSON-Genome-Format

Once you have a .json file, you can load it into IGV via Genomes > Load Genome from File or Genomes > Load Genome from URL

[Luigi Marongiu]

Thank you, I saw that file but (1) how do I generate the Json file in the first place (not manually that is)?, and (2) where do I get the annotations for this bacterium? 

PS: it might be that the genome already loaded in IGV is the same than the one I am using, but the procedure is good for other occasions.

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[igv-help]

It's not clear to me what you are requesting, you asked for "custom annotation",  but maybe you are asking for a new assembly (sequence + annotation).   The genome json file is for specifying a new assembly,  and optionally annotations.

There is no automated way to create the json file,  you need to create it.   RE annotations, NCBI and UCSC are good sources.    If they aren't there perhaps contact the lab that generated the assembly.

We are working on a method to automatically add any genome available from UCSC's GenArk site:  https://hgdownload.soe.ucsc.edu/hubs/,  but this will not be available until later this year.  However I don't your assembly listed there.    If you find it listed with a different accession number let us know.

[Luigi Marongiu]

Thank you. With 'custom' I meant define a new seqeunce+annotation,
sorry for the misunderstanding.

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Best regards,
Luigi