Genome of interest

[susheel raina]

Hi, 

My genome of interest (Prunus dulcis: Almond) is not there in the genome list. Will IGV help group please add the same in the genomes' list.

Thanx

Susheel

[robin...@gmail.com]

We will consider it but need a pointer to (1) a fasta file, and (2) an annotation file in gff, gtf, or bed format.

[susheel raina]

1. Fasta file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/201/215/GCF_902201215.1_ALMONDv2/GCF_902201215.1_ALMONDv2_genomic.fna.gz

2. Annotation file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/201/215/GCF_902201215.1_ALMONDv2/GCF_902201215.1_ALMONDv2_genomic.gff.gz

Hope my request is considered favourably as early as possible.

Regards

Susheel

[robin...@gmail.com]

Did you try just loading these from your local computer>.  Just download and gunzip the fasta,  the use. "Genome > Load from file..." to load it.   Download the gff and load it from the File menu. (File > Load from file...). 

[susheel raina]

Hi Robin. 

I have downloaded the file and it is a GZ type file format not fasta. How to gunzip it?

regards

[James Robinson]

On most computers just double-clicking it will gunzip it.  Otherwise you might have to install a program to do it.

[susheel raina]

Hi Robin,

I tried to upload but failed. Please help me load the genome.

Regards

Susheel

[Helga Thorvaldsdottir]

Susheel,

I was able to load into IGV both the fasta file and the gff file that you linked to in an earlier message in this thread. 

Make sure to load the fasta file via the Genomes menu (Genomes > Load genome from file), and the gff file via the File menu (File > Load from file).

If they do not load for you, make sure you are not using an old version of IGV.

Note, when you load the gff file, IGV does pop up a message recommending an index file be created, you can follow the directions to do that, but the file loaded ok without it.Also, you may want to right-click on the gff track once it's loaded and select "expanded".

Helga

[susheel raina]

Thanks Helga,

I was struck at this point. Your help is much appreciated.

Now I can give a try for my data on IGV.

Thanks again.

Best regards

Susheel

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[susheel raina]

Hi Helga,

Thanks for guiding. I could load the genome. But in does not appear in the drop down menu of the genomes list. Please add it to the list of genomes displayed on the software window.

Regards

Susheel

[Helga Thorvaldsdottir]

Hi Susheel,

I don't know why it doesn't appear in your genome dropdown menu, unless you've recently reset your <home>/igv folder. 

The contents of the folder <home>/igv/genomes defines what you see in the dropdown menu; it stores information about the genomes you have loaded, and any genomes you've loaded via file/url will be listed in the file user-defined-genomes.txt . See the screenshot below of what I see in my menu after loading your genome of interest. 

If you've cleared out any of these folders/files, you'll need to load your genome again via file/url so IGV can again log them there for the menu. 

Note that your genome will not appear in the Genomes > Load Genome From Server list, as that will only display genomes hosted by IGV.

Helga