FORUMTranscriptomics workflow in galaxy
Karen Gonçalves demandée il y a 1 an



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.
https://galaxy-1hge11q-12qm.udes.genap.ca/galaxy/u/karencgs/w/transcriptomics-workflow

Thanks for the help.
Karen

1 Réponses
flefebvre personnel répondue il y a 1 an



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

flefebvre personnel répondue il y a 1 an

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

Karen Gonçalves répondue il y a 1 an

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 personnel répondue il y a 1 an

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