Cellranger data to Monocle Pseudotime

Question

[Payal]

Hi,

How to convert 10X data to do psedotime analysis using Monocle. All the tutorials in Monocle point to cellranger kit which has been deprecated. I followed - https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices and https://kb.10xgenomics.com/hc/en-us/articles/360023793031-How-can-I-convert-the-feature-barcode-matrix-from-Cell-Ranger-3-x-to-a-CSV-file-?source=search to get to a matrix. Bu I am not sure if this is the right way?

Also there is an option to convert data from Seurat object to Monocle newCellDataSet object?

Anyone done this before?

Thanks, Payal

[Lior Pachter]

Here is a tutorial for how to convert 10x data to Monocle pseudotime: https://colab.research.google.com/github/pachterlab/kallistobustools/blob/master/notebooks/kb_monocle.ipynb

The tutorial goes from reads to results, and is on Google Colab so you can run it in a browser.

Answer 1

[jared.andrews07]

Where did you see that cellranger is deprecated? It is still very much in use. Monocle3 supports the standard cellranger output, you don't have to mess with it at all.

[swbarnes2]

The 10xGenomics R suite used to do things like aggregate samples, and between adding Loupe and adding functions to cellranger, the R suite is deprecated.

[jared.andrews07]

Oh, I never even knew they had an R suite. Just use the command line version, it supports aggregation now too.

[Payal]

Yes I used normal cellranger aggr to aggregate samples but they used to have this cellranger R kit to easily transform data into an R matrix type object, which they no longer support. So I am having this confusion because now they output everything as barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. And then the data needs to be transformed. So I followed the above links as directed by 10X customer support.

[jared.andrews07]

Please read the link in my answer - all you have to do is point Monocle to the folder with those file in it. It should have no trouble importing the information.