ucsc genome browser for non-model organism (Buffalo= Bubalus bubalis)

Question

[mostafarafiepour]

Hi Dear all,

I am analyzing the genome of the Buffalo. I calculate Fst using VCF file. Then, I convert the Fst file to a wig file for submit in the ucsc genome browser to identify the candidate genes. But in ucsc genome browse Buffalo genome was not defined.

What is the best idea to solve this problem?

Best Regard

Answer 1

[vkkodali_ncbi]

You can consider using NCBI Genome Data Viewer (https://www.ncbi.nlm.nih.gov/genome/gdv/?org=bubalus-bubalis&group=cetartiodactyla) with which you now have the ability to load and view bigWig files. See: https://www.ncbi.nlm.nih.gov/genome/gdv/browser/help/#managing-userprovided-and-remote

[mostafarafiepour]

many thanks for your reply,

This is a good option. But I did not understand how to load the Wig file??

[GenoMax]

From second link above:

Remote Streaming Files

BAM, bigBED and bigWIG files hosted at remote locations can be streamed for display in GDV. 
To add these data as tracks, select "Add Remote Track" from the Options menu, and enter the corresponding URL in the display

Note: BAM files hosted on HTTPS and FTP are not yet supported.

So if you don't have a way to host them on a web location you won't be able to use GDV. Looks like wig format files are not supported.

[vkkodali_ncbi]

Wig files can be uploaded directly. From the 'User Data and Track Hubs' on the left hand side, you can use Options > Add Files to upload a wig file from your computer. See: https://www.ncbi.nlm.nih.gov/genome/gdv/browser/help/#UPLOAD

It helps if you have a 'My NCBI' account in a situation like this. Any files you upload will then be available in GDV accessed from a different computer. Note, files uploaded in this manner are automatically deleted after a certain period of time.

[mostafarafiepour]

Thanks very much for your good guidance. I uploaded the wig file, The wig file format is as follows.

track type=wiggle_0 name=Fst_RJFsComs description="Fst_RJFsComs" maxHeightPixels=40:40:11 visibility=4
fixedStep chrom=chr1 start=1 step=20000
0.0911881
fixedStep chrom=chr1 start=20001 step=20000
0.105657
fixedStep chrom=chr1 start=40001 step=20000
0.115868
fixedStep chrom=chr1 start=60001 step=20000

As I said before, I created the wig file from the Fst file. And from the Fst file I created the following plot.

so, i want to accurately find the genes for the specified peaks, for example, in chromosomes 12 and 18 and 24.

Now, After uploading the wig file, I've seen the following results.

[vkkodali_ncbi]

Something is not right with the wig file. Based on the wiggle format specs (https://genome.ucsc.edu/goldenPath/help/wiggle.html) your wig file should display a peak of height 0.0911881 at position 1 on chromosome 1. After loading the data, I do see the peak at that position in GDV. The lowest scale GDV tracks of this type can go to is 1. Same for position 20001. So, unless you zoom in to the sequence level, you cannot see the peak.

[mostafarafiepour]

Can you tell me exactly where my file is false? But it looks like everything is fine after uploading the file. Please see the photo in the attachment. (for Chr24)

[vkkodali_ncbi]

Nevermind, I saw the plot from Fst file and assumed that's how the data for just chr1 was supposed to look like. I realize now that that plot has data for all of the chromosomes. Does your data have negative values?

[mostafarafiepour]

Yes, as you mentioned, I have 24 chromosomes. yes my data have negative values.

-0.689784143333663
-0.891484952281155
-0.577899738408206
1.74299980785602
1.0806614787567
0.945672420598925