If I want to analyze single cell RNA-Seq data in Galaxy, what is the best pipeline to use? I've been looking for an answer to this all over the internet, and it appears hard to answer. I'm new to the field, so any advice would be helpful.
I ran Tophat, so I have mapped reads and I've run Cufflinks, but I was told this may not be the best pipeline to follow and I have no problem backing up.
Further, if I'm interested in differential expression, should I treat each cell (Tophat file) as a different "condition"? Also, is there any simple way to get an expression matrix from a Galaxy program that I can then run on outside programs (such as homemade R packages)?