Question: Cellranger data to Monocle Pseudotime
0
gravatar for Payal
8 months ago by
Payal90
Payal90 wrote:

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

ADD COMMENTlink modified 8 months ago by jared.andrews077.5k • written 8 months ago by Payal90
1

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.

ADD REPLYlink written 8 months ago by Lior Pachter540
0
gravatar for jared.andrews07
8 months ago by
jared.andrews077.5k
Memphis, TN
jared.andrews077.5k wrote:

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.

ADD COMMENTlink written 8 months ago by jared.andrews077.5k
1

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.

ADD REPLYlink written 8 months ago by swbarnes28.9k

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

ADD REPLYlink written 8 months ago by jared.andrews077.5k

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.

ADD REPLYlink written 8 months ago by Payal90

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.

ADD REPLYlink written 8 months ago by jared.andrews077.5k
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