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Question: Tophat is deprecated; use replacement mapper HISAT2
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gravatar for bazghazia7
28 days ago by
bazghazia7 • 0
bazghazia7 • 0 wrote:

Hi, I cannot see tophat in RNA analysis tool please guide me who is the error and how should I resolve it.
tophat galaxy deprecated hisat2 • 71 views
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modified 28 days ago by Jennifer Hillman Jackson ♦ 25k • written 28 days ago by bazghazia7 • 0
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gravatar for Jennifer Hillman Jackson
28 days ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Tophat has been deprecated and the replacement tool is HISAT2. For a current example RNA-seq tool usage/workflow, please start here:

Galaxy Tutorials: https://galaxyproject.org/learn/

The tool is still on the Public Main server at https://usegalaxy.org in the tool panel for now. Use the search at the top of the tool panel to find it. Since the tool is deprecated, it may fail or produced odd results, so if you choose to use it, keep that in mind. Bug reports or questions do not need to be sent in as there will be no further changes or updates. Instead, switch to using HISAT2 going forward.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 28 days ago by Jennifer Hillman Jackson ♦ 25k
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