Basic Questions

Posted By: will_monty18, on Jul 25, 2019 at 11:36 AM

Hi everyone, 

I'm new to scRNA seq and I'm having some trouble with some basic things about data that CellRanger will accept. I have these files that I downloaded from GEO, but I'm not sure that they will work with CellRanger since they were created under the Mars-Seq2 protocol. In addition, I'm not quite sure what type of files they are, as they don't look like any FastQ files that I've ever seen. If someone could help me with 1, explaining if I CAN input these files into CellRanger; 2, if not what I need to change about them to do so, and 3, what type of files they are. Thanks in advance!


Re: Basic Questions

Posted By: 10xDave, on Jul 25, 2019 at 3:45 PM

Hi will_monty18,


Thank you for your question and interest in scRNA.  


Cell Ranger is designed and licensed to work on data from 10x libraries only. I'm not familiar with Mars-SEQ2, but searched around for you. You may want to try this tool instead.


If you are learning about scRNA, I would encourage you to learn more about our market leading10x Single

Cell products.


You can also download some sample 10x datasets that work with Cell Ranger here:







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