how to create custom genome with annotation in IGV ver. 2.11

[marina naoumkina]

Hello,

Can anybody provide instruction for biologist (not familiar with code writing) how to create custom genome by using genome sequence *fasta file and gene model description *gff3 file?

The new IGV ver. 2.11 does not have option to create annotated custom genome.

Thanks

Marina

[James Robinson]

Simply load the fasta in "Genomes > Load from file".   If its not indexed it will do that for you.   Then load as many gff3 files as you like via the File menu.    If you wish to save the combination of fasta and gff for later loading save it as a session from the file menu.

[Margot]

Hello!

I'm trying to import my custom genome but encountering issues. I first imported the genome using the command above (with indexing). I then did File-->Load from file-->selected sorted gff3 file. I am able to view the genome sequence, but do not see any genome features in the gff track. The chromosome names match between genome and gff file. What would you recommend trying next to load the gene annotations for my genome?

Thank you so much!

Margot

[James Robinson]

How large is your gff3 file? 

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[Margot]

Thanks for your response!

I noticed the sorted and regular gff3 files are different sizes--sorted gff is 22 KB, unsorted gff is 20.7 MB.

Thanks again,

Margot

[James Robinson]

Are you sure its 22 KB and 20 MB?  If so something is wrong, that's almost 100 times difference in size.

[Margot]

I just checked again, and that is correct. The sorted version is much smaller. Could there be an issue with the way this file is being sorted in IGV? I just did the sort upon import of GFF file when prompted. Selectedd function-->sort and clicked "sort". Interesting...I just tried to re-create this sequence in IGV by loading the unsorted GFF. It didn't prompt me to sort and the gene annotations loaded in the viewer. Do you know what could have gone wrong? Thank you so much!!

[Margot]

Sorry--to clarify--I think the initial issue was resolved by re-importing the unsorted GFF file. I'm at a loss as to what happened and how this fixed the issue (but glad it seems to!)

Thanks!

[James Robinson]

Don't know, but the sorting is only an optimization.  If it is loading fine without it just ignore that suggestion.

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[Anmol Wareh]

hello James

I followed the above instructions to upload custom genome. However, I am receiving the error message that either upload a json file or a fasta and an indexed file on web browser. and I am unable to download the desktop version. I am using Mac.

Thanks 

Anmol

[James Robinson]

Are you asking about igv desktop, or igv-web (at https://igv.org/app).   There is no concept of a ".genome" file for igv-web.   As indicated, you can just select your fasta and fasta index files (you must select both),  or load both by URL, to define the reference.   If you have annotation files you can then load those from the track menu.

You can also create a genome json file, and load that from the "genomes" menu, but that is a little more complex.     There is a description here. https://github.com/igvteam/igv/wiki/JSON-Genome-Format.

BTW, a technical point, but nothing is uploaded.   You are loading directly into your browser.

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[James Robinson]

Also,  importantly,  you cannot reference local file paths from the json file,  only URLs are supported.   This is a web security consideration enforced by browsers, there is nothing we can do about it,  local file paths cannot be used in javascript in a browser.