Question: adding genomes in igb
1
gravatar for jenyka_dm
5 months ago by
jenyka_dm10
jenyka_dm10 wrote:

Hi, I am trying to visualize the streptomyces hygroscopicus genome on igb. But IGB doesn't have this genome. I downloaded the genome from ensembl and NCBI, but I cannot load it into IGB (the file is a fa.gz file). Could you tell me how could I do that? Thanks!

ADD COMMENTlink modified 5 months ago by nowlan.freese20 • written 5 months ago by jenyka_dm10
1
gravatar for nowlan.freese
5 months ago by
United States
nowlan.freese20 wrote:

Hi jenyka_dm,

You need to unzip your fa.gz file. Depending on your operating system, you should be able to double-click on the file or right-click > unzip.

Then, to load the custom genome in IGB:

Select File > Open Genome from File... (or click the DNA icon in the Toolbar.)

  1. Select a sequence file to use as the reference genome (fasta or 2bit format).
    1. Optional: Enter an IGB-friendly genome version name (optional)
    2. Optional: Enter the species name, including genus, species and variety as appropriate (optional)
    3. Click OK and wait for the genome to load.
    4. Open data files as usual. And to view sequence, zoom in and click Load Sequence.
ADD COMMENTlink written 5 months ago by nowlan.freese20

Hi! Thank you for the advice! But it wouldn't let me unzip the file. The icon is also not of a zipped file though... It's just a plain paper instead of the folder with the zip....

ADD REPLYlink written 5 months ago by jenyka_dm10

Is there maybe a way that I could convert the formats?

ADD REPLYlink written 5 months ago by jenyka_dm10
1

IGB will recognize .fa files, so you should not need to convert the file.

What operating system are you using? The file should work if you are able to extract/unzip it.

ADD REPLYlink written 5 months ago by nowlan.freese20

Windows, when I right click on the file it doesn't even give me the option of extract/unzip. On the top of the window, where "extract" tab is, all options are unavailable...

ADD REPLYlink written 5 months ago by jenyka_dm10

I will try to use the link you have sent to extract again

ADD REPLYlink written 5 months ago by jenyka_dm10

Thanks you!! The link worked!!

ADD REPLYlink written 5 months ago by jenyka_dm10
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