12 days ago by
United States
Hello,
It sounds like something went wrong during this step, or possibly an upstream step: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#mapping-1.
Double check the settings/inputs and especially the target genome mapped against (rn6). Was the mapping job successful? Not just "green" in color, but does it have the expected content? Check these first: 1) Does the BAM output have the database metadata attribute rn6 assigned? If not, you likely mapped against the wrong reference genome. 2) Are there in fact hits in the BAM? A tool like Samtools > Stats generate statistics for BAM dataset is a good way to summarize the content. If there are no mapped reads, you'll need to do some detective work to find out which step (or steps) your usage differed from the tutorial and make corrections as needed.
If you cannot figure out the problem we can probably help to troubleshoot. It doesn't appear that you are working at Galaxy Main https://usegalaxy.org. If at another public Galaxy server, a share link to your tutorial history can be generated and posted back. Note the dataset number of the problematic BAM and be sure to leave all datasets in the analysis thread as active (do not delete or we won't be able to review them for upstream problems).
If not working at a public Galaxy server, you might try running through the tutorial at one to see if you get the same results. From this page https://galaxyproject.github.io/training-material/topics/transcriptomics/, the "Galaxy Instances" gear icon lists public servers where each tutorial is known to work. For this one, try Galaxy Europe https://usegalaxy.eu.
If you cannot reproduce the problem at Galaxy EU, there might be a configuration or resource problem at the Galaxy server you are working at, or you did some steps differently (correctly) in the tutorial rerun.
FAQs: https://galaxyproject.org/support/
Thanks! Jen, Galaxy team
