documentation for scATAC-seq data

[hejing3283]

Hi I am wondering if there is any documentation for 10x scATAC data?

[maximilianh]

sorry, do you mean the ATAC-seq mode in the cell browser? If yes, there is extremely little right now, because there is still a bug in it, but i'm happy to document it now and you can use it and can tell me if you find other bugs.

Is that's what you mean?

On Mon, Apr 5, 2021 at 8:43 PM Jing He @.***> wrote:

Hi I am wondering if there is any documentation for 10x scATAC data?

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[hejing3283]

Hi Maximilian,

Yes. I do meant ATAC-seq mode. It would be great if you could provide some examples on how to process it. Thanks a lot!

Best, Jing

On Mon, Apr 5, 2021 at 2:47 PM Maximilian Haeussler < @.***> wrote:

sorry, do you mean the ATAC-seq mode in the cell browser? If yes, there is extremely little right now, because there is still a bug in it, but i'm happy to document it now and you can use it and can tell me if you find other bugs.

Is that's what you mean?

On Mon, Apr 5, 2021 at 8:43 PM Jing He @.***> wrote:

Hi I am wondering if there is any documentation for 10x scATAC data?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/211, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AACL4TPI45PY44MFBVMT5W3THIAGRANCNFSM42NIMONA

.

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-- Cheers! Jing

[maximilianh]

Sorry, this required a new realease. Now that the release is out:

scATAC data needs a gene model so you can search for genes and get the closest peaks. you can use the tool cbGenes for this to download the gene model. I have ones for human and mouse now for your to download.

Do you know the gene models that you want to use? you can run "cbGenes ls". This shows a list of possible gene models. Is the one that you like among them?

[hejing3283]

Actually, I am working on both human and mouse gene model. Could you help to share what you have done so that I can convert scATAC data into the current browser format?

There is another browser (https://ctlab.github.io/SCE/) which could search either peak level infor or gene level information. I am just wondering if something similar could be achieved there?

Thanks a lot! Jing

On Mon, Apr 19, 2021 at 8:53 AM Maximilian Haeussler < @.***> wrote:

Sorry, this required a new realease. Now that the release is out:

scATAC data needs a gene model so you can search for genes and get the closest peaks. you can use the tool cbGenes for this to download the gene model. I have ones for human and mouse now for your to download.

Do you know the gene models that you want to use? you can run "cbGenes ls". This shows a list of possible gene models. Is the one that you like among them?

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-- Cheers! Jing

[maximilianh]

That's what we do: you can search for either genes or peaks: https://cortex-atac.cells.ucsc.edu/

If you enter a gene, it lists all the peaks nearby. If you enter a range, it shows the peaks in the range.

OK, let's start with human then. Which gene models do you use? Gencode? If yes, which version?

We just noticed that the current pip install does not have cbGenes, sorry, you can get it with pip install cellbrowser --pre now, otherwise we'll make a new release very very soon.

On Mon, Apr 19, 2021 at 7:35 PM Jing He @.***> wrote:

Actually, I am working on both human and mouse gene model. Could you help to share what you have done so that I can convert scATAC data into the current browser format?

There is another browser (https://ctlab.github.io/SCE/) which could search either peak level infor or gene level information. I am just wondering if something similar could be achieved there?

Thanks a lot! Jing

On Mon, Apr 19, 2021 at 8:53 AM Maximilian Haeussler < @.***> wrote:

Sorry, this required a new realease. Now that the release is out:

scATAC data needs a gene model so you can search for genes and get the closest peaks. you can use the tool cbGenes for this to download the gene model. I have ones for human and mouse now for your to download.

Do you know the gene models that you want to use? you can run "cbGenes ls". This shows a list of possible gene models. Is the one that you like among them?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/maximilianh/cellBrowser/issues/211#issuecomment-822442969 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAUAIIPTIMGCWGLKGVLFOFDTJQRV3ANCNFSM42NIMONA

.

-- Cheers! Jing

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[matthewspeir]

Hi, @hejing3283.

I've added some documentation now for how to set up an ATAC-seq browser like the one Max linked in his last comment: https://cellbrowser.readthedocs.io/en/master/howto.html#how-to-visualize-single-cell-atac-seq-data-in-the-cell-browser. Let me know if there is anything that is unclear in the steps.

Thanks!