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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Max number of single cells to create beat #81

Open znavidi opened 5 years ago

znavidi commented 5 years ago

Hi,

I would like to know what is the maximum number of single cells that snap ATAC could create bmat from (addBmatToSnap function)? I am merging 63 snap files containing more than 200,000 single cells and while running this function, after a while it will be killed. Is it possible to load such number of data with snapATAC?

Best, Zeinab

znavidi commented 5 years ago

I would be grateful if you share your experience with me about this issue :)

Best,

yasserIRCM commented 5 years ago

Hi, could you provide the error message you are getting?

regards

znavidi commented 5 years ago

it does not get any error. it is killed after some time. what do you think about it?

Best,

r3fang commented 5 years ago

Hi,

There is no problem for processing 200K cells, but concatenating 63 matrix killed the program by Matrix package. I did not anticipate this many samples to be processed at this moment, but will add another tutorial for processing many samples.

-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Aug 30, 2019, at 2:19 PM, znavidi notifications@github.com wrote:

Hi,

I would like to know what is the maximum number of single cells that snap ATAC could create bmat from (addBmatToSnap function)? I am merging 63 snap files containing more than 200,000 single cells and while running this function, after a while it will be killed. Is it possible to load such number of data with snapATAC?

Best, Zeinab

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znavidi commented 5 years ago

Thanks for your response. A tutorial would definitely be helpful!

Best

r3fang commented 5 years ago

hi, it will take a while to create the tutorial. at the same time, we can figure out another way to do it. Is it possible for you to create a binary matrix on your own that combines all the samples instead of using "addBmatToSnap"?

znavidi commented 5 years ago

Thanks for following up. I actually defined a function and analyzed and saved each of the samples' cell by bin matrix separately and it works for me :)

Best, Zeinab

r3fang commented 5 years ago

Great!

-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Sep 9, 2019, at 9:44 AM, znavidi notifications@github.com wrote:

Thanks for following up. I actually defined a function and analyzed and saved each of the samples' cell by bin matrix separately and it works for me :)

Best, Zeinab

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