FORUMTranscriptomics workflow in galaxy
Karen Gonçalves asked 2 years ago

So, I am created a workflow on GenAp Galax to analyse transcriptomic data. I am using TopHat2 to align my trimmed reads to Arabidopsis genome and I want to get a file with the unmapped reads. I selected all the outputs of tophat2 to be visible in my history, but the unmapped reads never appear.
Also, I tried everything to have the outputs of the tools carry the name of the input so I dont have to manually change each output name, but it doesn’t work.
Here is the workflow I am using.

Thanks for the help.

1 Answers
flefebvre Staff answered 2 years ago

Hello Karen, did you select “yes” under:
TopHat settings to use ->Full parameter list -> Output unmapped reads -> YES

flefebvre Staff replied 2 years ago

Also I cannot access your history despite having a GenAP account.

Karen Gonçalves replied 2 years ago

Thanks for the help, I edited the workflow and checked yes in that box. But now my history is not loading and at my genap page it says the galaxy app is “starting” for a week now.
So I still can’t check if it solved the problem.

flefebvre Staff replied 2 years ago

Hi Karen, unfortunately people on this forum cannot help you with GenAP technical issues. Please contact to inquire about the status of your jobs. Perhaps it just happens the cluster was very busy.