Hello Peggy,

The reference genome named simply "arabidopsis" in Galaxy is a legacy genome name and may not work with all tools. Assigning the reference genome name "Arabidopsis_thaliana_TAIR9" instead is the recommended choice (both are TAIR9).


The next item to change is the format of the chromosome names, specifically the capitalization. The file you loaded has chromosome names like "Chr" and in both the "arabidopsis" and "Arabidopsis_thaliana_TAIR9" genomes on the Galaxy main server, the chromosome names are like "chr".

Reassigning the database and correcting the capitalization in the input file may resolve the issue.

Another choice is to load the reference genome you used to generate the data into your history in fasta format, and use it as a custom genome for visualization.

If you need help with any of this, please let us know,

Best,

Jen
Galaxy team

On 11/9/11 9:33 AM, wu yijin wrote:
Hi All,

I am new of Galaxy. I want to visualize my short mapping results in the
browser.
I uploaded my .wig file which has format as this, (first column is
position, second is the read soverage of that position)

variableStep    chrom=Chr1
4       1
5       1
6       1
7       1
8       2
9       3
10      3
11      3
12      3
13      3
14      3
15      3
16      4
17      4
18      4

But it comes an error
Couldn't open 
/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/arabidopsis.len ,
No such file or directory

Does anyone know how to fix this?
Many thanks!

Best,

Peggy


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___________________________________________________________
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