2.6 years ago by
This is our RNA-seq tutorial. https://wiki.galaxyproject.org/Learn/GalaxyNGS101#Reference-based_RNA-seq
To learn Galaxy in general, please see: http://usegalaxy.org/galaxy101
Any output in tabular format can be filtered with tools like Filter and Select. This can be downloaded and imported into Excel.
For downstream analysis, there are many choices. Search by keywords to find tools ("gene ontology", etc). Make sure they are appropriate for RNA-seq (not Variant analysis). Usage is on the tool forms and there are practical examples in the second tutorial linked above.
For example, use common gene name identifiers in the results to associate content with external data sources using tools like "Join two Datasets/Compare two Datasets". This method will only work if you incorporate an appropriate reference annotation in Cuffdiff. iGenomes is one good source for reference annotation. There are many posts on this forum about RNA-seq annotation and the capture of gene ids - a search will find them.
Best, Jen, Galaxy team