I created reference using the genome and gtf file successfuly. But when I am trying to use rsem_calculate expression, the reference created and all the bam file are unavailable. These files are available for other tools.
Welcome, @Aasim_Majeed
To prepare the reference input for RSEM calculate expression, use the tool RSEM prepare reference.
This create a file with the datatype rsem_ref that you can choose to select from the history.
If that is what you have done, but the tool form is still not seeing the file, check the following first, then considering sharing back more details. Maybe there is a bug.
I’m guessing that the first item here is what is going on.
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Make sure that the history with the data you want to use is the active history before you load up the tool form. Switch at the top of the history panel using the multi-select icon or go to User > Histories. FAQ: Finding Histories.
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Make sure to click on the input select function icons to search for a file (“dataset”) versus a folder (“collection”) to match your data.
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Make sure the datasets you want to use are not hidden. For collection input, just the top level folder needs to be active and the files inside can be hidden.
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The datatype of the files should match what is shown on the tool form. This is a sanity check filter – when a dataset matches the filter, it will be available to choose.
How to share more details about the problem if you are still stuck → How to get faster help with your question. Screenshots would probably help with this one. Expand the datasets to show the datatypes please, and make sure the server URL shows up somewhere or just confirm this is at UseGalaxy.eu. The tool version might also matter so include that as well please (tool/version is at the very top of the form, or on the job details page).