Question: Where is "Tophat for illumina Find splice junctions"?
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gravatar for xinbo961
14 months ago by
xinbo9610
xinbo9610 wrote:

Dear Sir/Madam:

This is Bob. I am interested in the course of RNA-seq-analysis-mapping. The demo video showed that "Tophat for illumina Find splice junctions using RNA-seq data" was used for RNA-seq analysis. But It was not found under NGS: RNA Analysis. I need your help. Thanks a lot.

Best, Bob

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ADD COMMENTlink modified 14 months ago • written 14 months ago by xinbo9610
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gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Was this the reference tutorial video? https://www.coursera.org/learn/galaxy-project/lecture/VxxpN/rna-seq-analysis-mapping

The tools used in this tutorial are available at the Main Public Galaxy server http://usegalaxy.org. Which one is missing? Tophat for Illumina has been replaced with Tophat2 (named simply Tophat). If another tool is missing, it may be in other tool groups. Search by the tool name (top of the left tool panel) to locate. The Coursera tutorial is great to learn with plus there are other current RNA-seq tutorials for Galaxy that can be found here: https://galaxyproject.org/learn/

If working on a local or cloud Galaxy, any missing tools may need to be installed, by you or the administrator of the server.

If working at another Galaxy server (public or at your institution), you could ask the administrators of that server if the tools needed could be added. Note that many public servers are customized for a specific analysis workflow and may not include RNA-seq tools (and in many cases will not be modified).

For many use cases, Tophat has been replaced by HISAT when performing RNA-seq analysis. Please see the latest Tophat and HISAT release notes for details and links to related publications and user manuals. HISAT2 is available at http://usegalaxy.org and is in the Galaxy Toolshed where it can be installed in a local/cloud/another Galaxy server. The best practice workflow may have been updated since any tutorial you find was published, yet the original tools are still available (on the server you are using, or in the Tool Shed) if you wish to use the original methods.

We hope this helps. Please let us know if you need more information. Thanks! Jen, Galaxy team

ADD COMMENTlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson25k
0
gravatar for xinbo961
14 months ago by
xinbo9610
xinbo9610 wrote:

Hi, Jennifer: Thanks.

Yes, the reference tutorial video is https://www.coursera.org/learn/galaxy-project/lecture/VxxpN/rna-seq-analysis-mapping. According what you said, I searched by the tool name "Tohpat " at the top of the left tool panel (in https://usegalaxy.org). I got the tool names: "TopHat Gapped-read mapper for RNA-seq data", and "Tophat Fusion Post post-processing to identify fusion genes" and "HISAT A fast and sensitive alignment program". But there were three tool names: "TopHat Gapped-read mapper for RNA-seq data", "Tophat Fusion Post post-processing to identify fusion genes" and "Tophat for illumina Find splice junctions using RNA-seq data" in the reference tutorial video. So the tool "Tophat for illumina Find splice junctions using RNA-seq data" was missed. I want to to follow the video to finish my courses. Which tool can I use? Your help will be greatly appreciated.

Best, Bob

ADD COMMENTlink written 14 months ago by xinbo9610

Hi Bob,

The tool Tophat for Illumina has been deprecated and is no longer available at http://usegalaxy.org. Use the tool TopHat Gapped-read mapper for RNA-seq data instead. The output from this upgraded version of Tophat also includes a dataset of splice junctions. For the purposes of the course, using the default parameters with this version of the tool is also fine.

If you really want to use the older version of the tool, Tophat for Illumina, this would require setting up a local or cloud (AWS) Galaxy and installing the tools in the course. The public Galaxy instance at http://usegalaxy.org changes over time (available tools, user interface features, and the like). Alternative ways to use Galaxy are explained in the Introduction section for the course with more details in week 4, module 5. Supplemental to that are the resources at http://galaxyproject.org under "Choices" https://galaxyproject.org/choices/

For your own data analysis (beyond learning), using the latest version of the Tophat tool would be recommended.

Take care, Jen

ADD REPLYlink written 14 months ago by Jennifer Hillman Jackson25k
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