Problem with Reference genome from history in Tuxedo

Question: Problem with Reference genome from history in Tuxedo

9 months ago by

vsafavi • 0 wrote:

Hi,

1- I am using Tuxedo for tomato. I run the workflow from the shared data.

In the TopHat section in Tuxedo there are the following sections:

Output dataset 'output' from step 1 Use a built in reference genome or own from your history Use a built-in genome Select a reference genome If your genome of interest is not listed, contact the Galaxy team TopHat settings to use

However, it is not possible to choose any option for built in reference genome or from your own history. This is written just in the text format and I am not able to choose any of them - I need "from your own history" option.

2- Alternatively, I tried to use TopHat - not form tuxedo - but form the tools section, but the job list stays grey - not yellow or green - and it seems it does not work at all.

Many thanks in advance,

rna-seq queue tophat2 custom-genome hisat2 • 266 views

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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by vsafavi • 0

9 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I am not sure where you are using a tool named simply "Tuxedo". Tophat/Tophat2 are considered deprecated (all versions). HISAT2 is a better choice. Example tutorials with usage explained:

https://galaxyproject.org/learn/
RNA-seq: Introduction - an introductory tutorial for transcriptome analysis.
RNA-seq: Discovering and quantifying new transcripts - an in-depth transcriptome analysis example.

This is how to format a Custom Genome and promote it to a Custom Build:

Jobs run at the public Galaxy Main server https://usegalaxy.org will queue (remain grey) until resources are available. The queue can take up to 24 hrs but usually is much quicker.

Datasets and how jobs execute

Jobs run at other public or private Galaxy servers may have different methods for handling job queues - you should contact the administrators of the server you are working on to find out of there is a problem.

Publicly Accessible Galaxy Servers

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k

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