Single-cell RNA seq for bovine
0
0
Entering edit mode
9 days ago
Fatemeh ▴ 20

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.

reference Bovine RNA bovine seq genome Single-cell • 218 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

OP while true this will involve non-trivial work to create cellranger indexes etc. So that will add time/effort.

ADD REPLY

Login before adding your answer.

Traffic: 2249 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6