Hi, I am using a publicly available workflow for atac-seq analysis however it requires input of reference genome that can only be selected from the dropdown list. My species is not on the list and I have uploaded the reference genome found online to the custom build data however am unable to input that into the workflow?
Any help would be appreciated,
Kanisha
Welcome, @shahkanisha
The workflow probably needs to be adjusted to use a reference genome “from the history” instead of a genome pre-indexed on the server.
Try this
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Prepare your custom genome fasta → FAQ: How to use Custom Reference Genomes?
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Go into the workflow editor, and add a new input dataset for your custom genome fasta file.
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Next, click on the tool that will consume the custom genome. In the right panel, scroll down to the parameter for the genome selection, and adjust the reference genome choice to use a fasta from the history.
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Connect your new fasta input to the tool you adjusted.
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Save your workflow and give it a test run.
More workflow tips → https://training.galaxyproject.org/training-material/faqs/galaxy/#workflows
Hopefully this helps! Should you have problems, you can share back some screenshots about how those items above were set up, or a link to the workflows (original + adjusted) and explain what is going on.
Custom builds are only used for the built-in genome browser unfortunately. As @jennaj said there is another option to use a fasta file from your history, but I would recommend checking with the workflow authors first if they can help you. If the creator of the workflow is the IWC you could ask in Issues · galaxyproject/iwc · GitHub.