Pygenometracks: Changing bed style from flybase to UCSC

Hi. I want to change the bed style of my genes from flybase to UCSC format in galaxy using pygenometracks. Even though I try to set it to UCSC bed style the output is always flybase. I would appreciate any help. Thanks.

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Hi @MzwaneleN

This could be an input content problem, a tool option problem, or a previously undetected tool bug.

First, make sure you are using the most current version of the tool. Right now that is: pyGenomeTracks plot genomic data tracks (Galaxy Version 3.5)
. If using a different version, try this one and see if that resolves the issue.

If the problem persists, a few more details would help. Where are you running the tool? A public Galaxy server? Which URL? Or explain if somewhere else – and maybe try at a public Galaxy server to see what happens as a comparison – if it works at a usegalaxy.* server but not your own server, that narrows down what may be going wrong.

Let’s follow up from there.