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igvteam / igv-webapp

IGV Web App
https://igv.org/app
MIT License
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To upoad in IGV it says Genome requires either a single JSON file or a FASTA file & index file #263

Closed susheelskuast closed 1 year ago

susheelskuast commented 1 year ago

Dear All, I am a novice in handling genomic data and i want to browse quinoa annotated genome through IGV but i am unable to do it. Let me tell the series of actions that i am doing.

Going to the NCBI link and dowloaded the assembly in fasta format also and downloaded all the .fna and json files also but still IGV says "Genome requires either a single JSON file or a FASTA file & index file" Following is the link for the genome. https://www.ncbi.nlm.nih.gov/assembly/GCF_001683475.1/

please help me with line to line procedure for vewing/browsing the genome through IGV. I am very new to genomics and bioifnormatics. This i am doing to carry Association Mapping in Quinoa.

jrobinso commented 1 year ago

As a first step you need to define your reference genome by loading an indexed fasta file from the "Genome" menu. You can download the reference file from NCBI but will need to create an index with another tool, for example "samtools". A web search will help there The index file will have the same name as the fasta file, but with an added extensino ".fai" at the end.

After defining the reference you can load additional annotation files from the "Tracks" menu.

It's possible igv-webapp is not the tool you need, it does require some basic genomics and bioinformatics knowledge. The UCSC has pre-built browsers for all or nearly all NCBI assemblies with many annotations and other tracks already uploaded and ready to use. For your genome the link is https://genome.ucsc.edu/h/GCF_001683475.1. Please give that a try.

susheelskuast commented 1 year ago

Thank you jrobinso (https://github.com/jrobinso) for your reply. Yes, i gave a try and I am able to look for my requirements in https://genome.ucsc.edu/h/GCF_001683475 Is it possible to create index file (for the genome information available on NCBI) using GUI or Windows? or we have to do the same in command line only?

jrobinso commented 1 year ago

You can index a fasta with IGV desktop, which you can download here: https://software.broadinstitute.org/software/igv/download. From the menu select "Tools > Run igvtools...". Then select "Index" from the Command pulldown, select your fasta file, and click "Run". You must leave this window open until it completes. The fasta contains your reference sequence only, preparing other files can be more complex. I suggest you use the UCSC browser link referenced above.