I've seen R and python code for doing this conversion, but (for setting up a pipeline) is there an established command-line utility and galaxy tool for converting the split-seq output (sparse matrix market format) into a format that can be supplied to the seurat galaxy wrapper (which appears to take a gene by cell tsv)?
I wrote a quick perl one-liner to do the conversion myself, but when I supplied it to seurat, it complained about duplicates. What constitutes a duplicate? The genes and cell IDs are all unique. Perhaps I got some detail of the format wrong?