snATAC seq expression matrix

[Parul-Kudtarkar]

Hi,

In case of https://cellbrowser.readthedocs.io/tabsep.html - What does the expression matrix look like for snATACseq assays? Would binary accessibility matrix work?

Thanks! Parul

[maximilianh]

Hi Parul,

I've never worked with one, but I think, mostly yes. Do you have an example of such a matrix? You can send it to my personal email address (max@soe.ucsc.edu) and I can promise I won't share it. I'm interested in supporting such data and can work with you to adapt the viewer (e.g. showing outlinks from the cell browser to the genome browser that connect automatically to a the track hub with your coverage data)

Max

On Wed, Feb 27, 2019 at 8:28 AM Parul Kudtarkar notifications@github.com wrote:

Hi,

In case of https://cellbrowser.readthedocs.io/tabsep.html - What does the expression matrix look like for snATACseq assays? Would binary accessibility matrix work?

Thanks! Parul

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[Parul-Kudtarkar]

Hi Max,

Any updates on visualizing snATACseq assays? Example data - https://www.ncbi.nlm.nih.gov/pubmed/29434377

Thanks! Parul

[matthewspeir]

Is snATAC-seq similar to scATAC-seq? If so, then there are some scATAC-seq datasets in ArrayExpress here: https://www.ebi.ac.uk/arrayexpress/search.html?query=scatac-seq.

[maximilianh]

Parul thanks for the reminder ! I got stuck at the matrix conversion step, this format is really unusual. Apart from the format everything else should work. Parul, are you an R user ? I may have a question later...

On Wed 3 Apr 2019 at 18:32, Matt Speir notifications@github.com wrote:

Is snATAC-seq similar to scATAC-seq? If so, then there are some scATAC-seq datasets in ArrayExpress here: https://www.ebi.ac.uk/arrayexpress/search.html?query=scatac-seq.

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[Parul-Kudtarkar]

@matthewspeir yes, snATAC-seq is same as scATAC-seq

@maximilianh thanks for getting work started on the single cell ATAC-seq data to cell browser I haven't used R in my recent projects but I will try my best to answer questions you may have. Thanks!

[maximilianh]

Parul so you’re using mostly python ? May I asked how you converted the matrixes that you sent me ?

On Wed 3 Apr 2019 at 19:43, Parul Kudtarkar notifications@github.com wrote:

@matthewspeir https://github.com/matthewspeir yes, snATAC-seq is same as scATAC-seq

@maximilianh https://github.com/maximilianh thanks for getting work started on the single cell ATAC-seq data to cell browser I haven't used R in my recent projects but I will try my best to answer questions you may have. Thanks!

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[Parul-Kudtarkar]

@maximilianh the files were generated by another group & they used R https://github.com/r3fang/snATAC To generate binary accessibility matrix see step 6 in the above pipeline. The files are massive & sparse matrices

[maximilianh]

Sorry I don't know what a "binary accessibility matrix" is. Why can't I use the matrices as they are? They look OK, just the text format is weird, not the matrix itself. I don't know enough about scatacseq, sorry!

On Wed, Apr 3, 2019 at 11:18 PM Parul Kudtarkar notifications@github.com wrote:

@maximilianh https://github.com/maximilianh the files were generated by another group & they used R https://github.com/r3fang/snATAC To generate binary accessibility matrix see step 6 in the above pipeline. The files are massive & sparse matrices

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[Parul-Kudtarkar]

That works too, thanks!

[Parul-Kudtarkar]

@maximilianh Max, did the expression matrix(binary matrix) for above data-set(see attached) work out of the box? GSM2668117_e11.5.nchrM.merge.sel_cell.mat.zip Thanks!

[Parul-Kudtarkar]

@maximilianh just confirmed that binary matrix works!

Also, for minimal conf - https://github.com/maximilianh/cellBrowser/blob/master/sampleData/mini/minimal.conf alpha = 0.3 parameter is required, or else it throws exception internal error: alpha is not defined internal error: cannot draw if coordinates are not set yet

Thanks!

[maximilianh]

Parul, sorry that I don't always reply immediately, I saw your message but didn't reply.

a) what is the github link that you sent me? It's the same file as the one in GEO. To load it into the cell browser, did you prefix it with the genome-regions and added the barcodes?

b) as for the alpha value, it should not be required at all... it used to be, but I changed that around 3-4 months ago. Can you give me a concrete example of your config file and possibly the matrix that you used?

It's great to hear that it worked. I'd like to reproduce it myself though to understand the application better and how these matrices could be shown better...

[maximilianh]

BTW: do you usually annotate the genomic regions with their neighboring genes?

[Parul-Kudtarkar]

Max, No worries.

That was the cellBrowser minimal.conf from the cell Browser repository

The expression matrix barcodes added 1st columns - Genes other columns is binary matrix

metadata 1st col barcode 2nd col clusters

UMAP coordinates bar code and corresponding coordinates

[maximilianh]

Thanks! May I ask how you obtained the clusters? I imagine you didn't use the cbScanpy pipeline but your own processing?

[Parul-Kudtarkar]

Max, Here is the snATAC seq pipeline - https://github.com/r3fang/snATAC