null for rownames(proj)

[ellyhung]

First of all, excellent work! Congratulations!

I have faced an issue trying to reproduce your analysis. In line 52 of script in snATAC_seq/data_integration)/05_clustering.ipynb, it seems that rownames(proj) is null as attched. I am wondering if I missed something here. I will be grateful for any response. Thank you in advance

[lzj1769]

Hi @ellyhung

Can you check if the proj is loaded?

[ellyhung]

Hi Zhijian, Thanks for the reply. Yes it is successfully loaded.  The only difference from my analysis to yours is that I used my dataset instead. But it shouldn’t be an issue since I processed all the steps as you provided and the outputs are in similar form as you shown. I checked the rownames. @.@rownames shows the sample names; while @.@rownames shows all the cell (format: samplename#sequence). 

On Thursday, March 23, 2023, 12:02 AM, Zhijian Li @.***> wrote:

Hi @ellyhung

Can you check if the proj is loaded?

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[lzj1769]

Hi @ellyhung

It's possible that ArchR updated the way it organized the data.

Anyway, here you can try an alternative way to get the cell names, but be careful that ArchR always adds the sample name to the barcode while Seurat doesn't.

[ellyhung]

Thank you so much for the information. Yes, that's possibly the reason.

In addition, I am wondering if I could know the reason that you remove cluster14, 22, 21, 26, 25 for annotation?

[lzj1769]

Hi @ellyhung ,

We removed these clusters because we found they were driven mainly by artifacts such as low data quality, patient-specific factors, high doublet score, etc, compared with other clusters.

And we couldn't identify these cells without clustering results available.

[ellyhung]

Thank you so much for your information!