Single-cell RNA seq for bovine
Dear All,
I would like to do single-cell RNA seq. However, I am not sure if I will not have any problem with availability of bovine reference genome and also if all the tools and R packages are available for the analysis of Bovine mRNA samples. How I can check these things?
If I know I will have issues with bovine then I can switch to human samples. It is just more feasible to get the bovine samples.
Thanks very much for your help.
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The bovine assembly and annotation look fairly good, so you shouldn't have a problem getting the initial feature UMI counts from Cell Ranger (or your preferred workflow of choice). After you have those the downstream analysis frameworks (i.e. Suerat, scanpy, bioconductor/OSCA) will mostly be species-agnostic.
OP while true this will involve non-trivial work to create cellranger indexes etc. So that will add time/effort.