Question: update drosophila genome to dm6
gravatar for huaqi.jiang
3.3 years ago by
United States
huaqi.jiang10 wrote:

The Drosophila genome has been updated to dm6. However, the Galaxy still only use dm3. Many gene annotations has been changed which caused a lot of headaches for figuring out the genes associated with particular ChIP-Seq peaks. Can someone update that in the Galaxy? I know how to map that ChIP-Seq data with custom genome, but all the tools such as bedgraph/bigwig still require a reference genome. Thanks.

galaxy • 1.1k views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by huaqi.jiang10


I have a fast file of dm6 which is correctly formatted to be used as a reference taken from the current history by most tools.  This might be useful in this manner  if you are not an administrator of your galaxy instance.

If you are an administrator you can make available to tools from the drop down  menus.

You can get the dataset  'dm6_iso_all' from the following shared history 

The other two datasets are the files from which this ref file was created (so you can check things yourself). the workflow used  was this one. 

If you are going to use this file you will want to be sure that it is correct !! Thanks Guy

ADD REPLYlink written 3.3 years ago by Guy Reeves1.0k
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Updating reference genomes on is a priority. Meanwhile, a Custom reference genome can be used with most tools. For those few tools that interpret the "database" attribute, create a Custom Build and assign that to the input datasets. 

How to:

Best, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
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