Question: Tophat can't see the build-in reference genome?
gravatar for vebaev
2.8 years ago by
vebaev130 wrote:

I successfully fetch an hg19 and build an bowtie2 index with Data managers. Bowtie2 can see the reference genome, but when I want to run a tophat job, there is no build-in reference genome on the drop down menu? Am I missing something?

tophat bowtie index • 930 views
ADD COMMENTlink written 2.8 years ago by vebaev130

I think this was recently fixed in a data manager, if you can be a little bit patient ... the data manager will be updated shortly, I guess.

ADD REPLYlink written 2.8 years ago by Bjoern Gruening5.0k

Thanks, so after some days I should uninstall and reinstall the index builder data manager to fix this or ?

ADD REPLYlink written 2.8 years ago by vebaev130
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Yes, re-running the Data Manager is how to add in the additional index. The option to include Tophat indexes was the recent change. Jen, Galaxy team

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson24k

Should I reinstall the DM?

ADD REPLYlink written 2.7 years ago by vebaev130
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