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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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