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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Merging snap objects #13

Closed andrewhill157 closed 5 years ago

andrewhill157 commented 5 years ago

I really love a lot of the ideas and functionality in SnapTools/SnapATAC, thanks for developing them both and congrats on the preprint!

Looking through the available functions, and am wondering if you think there might be a way to support merging of snap objects. I could obviously grab the binary matrices and merge them easily enough, but wondering if you think there might be a way to genuinely merge the objects so that all the other functionality in SnapTools could still be used as intended. The reason I ask is that we have several datasets that we have run in parallel to speed things up, but would be nice to be able to combine later for integrated analysis.

Thanks for the help!

r3fang commented 5 years ago

Hi,

Thank you for your kind message and thanks for try it! This is great question.

The answer is yes. SnapTools does not support merge of multiple "snap" files but "SnapATAC" supports to merge multiple snap object in R. Here is one example how SnapATAC analyzes two samples together here. You can merge multiple snap objects once they share cell-by-bin matrix of the same bin size. Last time i tried, I have no problem of merging up to 70 samples.

The reason that snaptools does not merge multiple snap files in to a single one is because I am trying to avoid creating a giant matrix that slows down the read-in function in SnapATAC. Also, as you mentioned, it would be nice to keep each sample separate so this can be ran in parallel.

Does it answer your question?

Best -Rongxin

andrewhill157 commented 5 years ago

Thanks so much, I hadn't noticed that tutorial, very helpful! All makes sense, will give it a shot and thanks again.

On Fri, Apr 26, 2019 at 9:24 AM Rongxin Fang notifications@github.com wrote:

Hi,

Thank you for your kind message and thanks for try it! This is great question.

The answer is yes. SnapTools does not support merge of multiple "snap" files but "SnapATAC" supports to merge multiple snap object in R. Here is one example how SnapATAC analyzes two samples together here https://github.com/r3fang/SnapATAC/blob/master/examples/10X_15k/10X_15k.md. You can merge multiple snap objects once they share cell-by-bin matrix of the same bin size. Last time i tried, I have no problem of merging up to 70 samples.

The reason that snaptools does not merge multiple snap files in to a single one is because I am trying to avoid creating a giant matrix that will slows down the read-in in SnapATAC. Also, as you mentioned, it would be nice to keep each sample separate so this can be run in parallel.

Does it answer your question?

Best -Rongxin

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/13#issuecomment-487117556, or mute the thread https://github.com/notifications/unsubscribe-auth/ABER4A2QEMVGDPVG3CYE2RDPSMUFBANCNFSM4HIW55KA .

r3fang commented 5 years ago

No problem. Thank you for trying! Please don't hesitate to contact me if you have any question!

r3fang commented 5 years ago

You might have seen this, but just want to bring this up in case. There is a session in the main page called FAQs which has answered some questions regarding the compatibility with 10X data. https://github.com/r3fang/SnapATAC

andrewhill157 commented 5 years ago

Awesome, thanks very much! Will let you know if I have any more questions and thanks again :)