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Question: Need help with "Tophat2" tool
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gravatar for plaza
3.8 years ago by
plaza • 0
plaza • 0 wrote:

I was trying to repeat one tutorial on RNAseq (RNASeqDGE_ADVNCD_Prep). In the TopHat2 section, I'm trying to align the reads to a built-in genome (saccharomyces cerevisiae sacCer2), but this genome does not appear in the available options. Any idea on what did I make wrong so far?

Thanks in advance!

 

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

 
tophat2 • 880 views
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modified 3.8 years ago • written 3.8 years ago by plaza • 0
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gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Load the genome from UCSC and then use it as a custom reference genome with tools. Here is how:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Best, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for plaza
3.8 years ago by
plaza • 0
plaza • 0 wrote:

Thanks Jen!
ADD COMMENT • link written 3.8 years ago by plaza • 0
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