Running Salmon on BAM files in Terra
I have BAM files generated from RNA-seq and stored on Terra and I'm looking to obtain pseudocount data for each sample using Salmon. Does anyone have experience using Salmon on Terra and can you suggest a workflow and any necessary inputs that would be needed to run it?
Hi Danny Jomaa,
Thanks for writing in. As a start, I would recommend browsing Dockstore and the Broad Methods Repository for workflows that use Salmon. Some may have documentation that will let you know how to run it or give you a better idea of how to use Salmon on Terra.
Here is a really good tutorial
Thanks for your reply! I went through both but unfortunately haven't found a workflow with documentation. For those I have found, I'm a bit unsure of the input parameters that are required by the workflow. That said, if you have any suggestions for a workflow or if I may have missed a well-documented one, please let me know!
Thanks so much! I'll take a look at that now.
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