Question: Need help with "Tophat2" tool - no chicken genome
0
gravatar for nico
3.3 years ago by
nico10
United States
nico10 wrote:

Hi,

I am new to Galaxy (which is great, thanks!) and I would like to use Tophat2 with chicken data. Unfortunately galgal4 (and other previous chicken genomes) are not in the built-in dropbox - unlike with Tophat 1.5. 
I looked on the forums etc. but it is still no clear to me how I should proceed if I still want to use Tophat2. What is the correct exact procedure to import my genome galgal4 such I could use it in Tophat but also later for some differential expression?

Thank you for your help.

Nic


 

Tool name: Tophat2
Tool version: 0.6
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/tophat2

 

galgal4 tophat2 chicken • 818 views
ADD COMMENTlink modified 3.3 years ago by Martin Čech ♦♦ 4.2k • written 3.3 years ago by nico10
1
gravatar for Martin Čech
3.3 years ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

Please see the wiki including the detailed page about reference genomes.

https://wiki.galaxyproject.org/Support#Custom_reference_genome

ADD COMMENTlink written 3.3 years ago by Martin Čech ♦♦ 4.2k
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