juliaolivieri
commented
4 years ago Hi Mason,
Our tool isn't currently compatible with Seurat, but we are interested in making it as widely usable as possible so we'll put this on our list of next steps software-development-wise. Glad to hear you're excited about using the tool!
Julia Olivieri
Hi there,
My name is Mason and I work as a computational biologist in the Orthopedic Hospital Research Center at UCLA. Our group has done extensive work analyzing alternative splicing as a regulatory mechanism in stem cell differentiation. We have used bulk seq as well as SMART seq for these analyses but would love to be able to annotate alternative splicing on the 10x single cell RNA seq platform. As such, we are very interested in your pipeline. I was wondering if your pipeline is compatible with downstream analyses on Seurat. I inquired with the Seurat developers about this first and this was their response. "We have not - but would encourage the authors, if interested, to submit a pull request to Seurat Wrappers demonstrating how to use their tool on a Seurat object." If this is at all possible I know that it would be greatly beneficial to the work that we are doing and for many other groups as well. I look forward to our communication and ultimately implementing your tool.
Best! Mason