Question: Cellranger on mac?
1
gravatar for aliceha23
6 months ago by
aliceha2310
aliceha2310 wrote:

This may be a stupid question, but how do people access cellranger..? By that I mean - it's only linux compatible, which I assume not a lot of people have on their computers, yet it's a very popular package, so I assume there's a workaround I'm not aware of? Is this something that people typically access through their sequencing facility? Or is it possible to run Cellranger on Mac and Windows machines? Again, sorry if this is a stupid question, new to scRNA-Seq and trying to analyze a dataset. Don't have access to core facilities due to COVID. I'm aware of other packages available, it just seems like Cellranger would be the huge timesaver.

rna-seq alignment • 459 views
ADD COMMENTlink modified 6 months ago by ATpoint40k • written 6 months ago by aliceha2310

You could install a virtual machine on your Mac and then run cellranger in that virtual machine. Since cellranger uses STAR for some of the alignments you will need to be able to allocate adequate resources to that virtual machine. It may be possible to run cellranger under WSL in Windows, in theory. But a virtual machine will work there as well.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax91k
2
gravatar for ATpoint
6 months ago by
ATpoint40k
Germany
ATpoint40k wrote:

CellRanger is resource hungry so I doubt many people really run it on normal PCs rather than powerful workstations or HPCs and on these Linux is (probably) the most popular operating systems. If you are really limited to any other platform then you can check for Docker images or setup Linux in a dual-boot fashion. Alternatives are pipelines such as Alevin or Kallisto|BUStools which are more memory efficient and faster as they rely on pseudoalignment/quasi-mapping.

Edit (10/20): STARsolo is an alternative to CellRanger which is faster and can produce (almost) identical output, not sure about memory requirements. Could be worth checking out.

ADD COMMENTlink modified 1 day ago • written 6 months ago by ATpoint40k
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