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colomemaria / epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python
BSD 3-Clause "New" or "Revised" License
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10X compatibility #85

Closed gaelcge closed 3 years ago

gaelcge commented 3 years ago

Hi guys I am wondering if you plan to do this in the next month ? "Soon available, there will be a tutorial providing a function to very quickly build custom count matrices using standard 10x single cell ATAC output." Thanks

DaneseAnna commented 3 years ago

Hi,

Yes !! This is already possible to build a custom count matrix from the cell ranger output ! Let me get back to you in the morning with more detail. But yes, this is now available.

Best, Anna

gaelcge commented 3 years ago

Hi Anna Thanks for your reply, it would be great to have the snippet of code that does it (i.e to build a custom count matrix from the cell ranger output) All the best Gael

On Mon, Mar 22, 2021 at 4:26 PM Anna Danese @.***> wrote:

Hi,

Yes !! This is already possible to build a custom count matrix from the cell ranger output ! Let me get back to you in the morning with more detail. But yes, this is now available.

Best, Anna

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/colomemaria/epiScanpy/issues/85#issuecomment-804370414, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFQDA6MU3QVO4L2DY2VGCEDTE6RW7ANCNFSM4ZTVLI3Q .

-- Gael Cagnone, Ph.D Computational biologist at the Montreal Single-Cell Academy CHU-Sainte Justine Research Center, University of Montréal s @.**@. https://www.joyallab.com/single-cell-academy https://www.joyallab.com/single-cell-academy New single-cell project? https://app.kognitions.com/projform/1567771615025x566347978085223900 [image: https://www.joyallab.com/single-cell-academy] https://www.joyallab.com/single-cell-academy

DaneseAnna commented 3 years ago

Hi Gael, Sorry for the delay. I got a little distracted on the way. Here is the tutorial to build a count matrix : https://nbviewer.jupyter.org/github/colomemaria/epiScanpy/blob/master/docs/tutorials/Tutorial_building_custom_count_matrices_from_tsv_or_cellranger_outputs.ipynb

There is a major update of the website coming up shortly and it will make the tutorial available there then. In the mean time it is available on Github.

Cheers, Anna

gaelcge commented 3 years ago

Thanks Anna, it would be great to have a tutorial which use the peak matrix from cellranger ATACseq (not MACS2). Looking forward to it! Gael