Closed gaelcge closed 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
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
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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
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
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