FORUMTranscriptomics workflow in galaxy
Karen Gonçalves asked 1 month 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.
    https://galaxy-1hge11q-12qm.udes.genap.ca/galaxy/u/karencgs/w/transcriptomics-workflow

    Thanks for the help.
    Karen

    1 Answers
    flefebvre Staff answered 1 month ago



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

    flefebvre Staff replied 1 month ago

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

    Karen Gonçalves replied 1 month 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 1 month ago

    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.