Skip marker annotation step?

[yeswzc]

Hi, I want to know if I can skip the step 9 in the example 10X Adult Mouse Brain. I am not sure because I see some steps which may add some objects to x.sp, including:

addBmatToSnap(x.sp);
x.sp = createGmatFromMat(...)
# normalize the cell-by-gene matrix
x.sp = scaleCountMatrix( ...)
# smooth the cell-by-gene matrix
x.sp = runMagic(...)

Should I perform those if I want to skip annotation?

Thanks!

[yeswzc]

Or, is it a bad idea to annotate all the genes in the genome? So, later, I can easily visualize any gene I like.

[r3fang]

yes! you can totally skip these steps if you don’t want to annotate the cluster

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

On Oct 1, 2019, at 10:27 AM, Zhichao Wu notifications@github.com wrote:

Hi, I want to know if I can skip the step 9 in the example 10X Adult Mouse Brain. I am not sure because I see some steps which may add some objects to x.sp, including:

addBmatToSnap(x.sp); x.sp = createGmatFromMat(...)

normalize the cell-by-gene matrix

x.sp = scaleCountMatrix( ...)

smooth the cell-by-gene matrix

x.sp = runMagic(...) Should I perform those if I want to skip annotation?

Thanks!

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[yeswzc]

Wow, that's cool.

1. But still a litter bit concerned. Step9 seems did some data normalization. Isn't it saved in the x.sp object and used in the downstream analysis?

2. By the way, is there a document describing the x.sp object?

Thanks!

[r3fang]

But still a litter bit concerned. Step9 seems did some data normalization. Isn't it saved in the x.sp object and used in the downstream analysis?

Step 9. performs count of cell-by-gene table and normalization. It is stored in the x.sp object. If you do not want to annotated the cluster, the cell-by-gene table will not be used for downstream analysis.

By the way, is there a document describing the x.sp object?

Current not but this is great suggestion! x.sp contains the following major object cell-by-bin matrix for clustering analysis cell-by-peak matrix for feature analysis cell-by-gene matrix for annotation and integration with scRAN-seq cell-by-motifi matrix for motif analysis

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

On Oct 1, 2019, at 5:22 PM, Zhichao Wu notifications@github.com wrote:

Wow, that's cool.

But still a litter bit concerned. Step9 seems did some data normalization. Isn't it saved in the x.sp object and used in the downstream analysis?

By the way, is there a document describing the x.sp object?

Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/109?email_source=notifications&email_token=ABT6GG6H4BW727SRNTDU4PTQMO5SFA5CNFSM4I4KKDEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEACZGXA#issuecomment-537236316, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG7L3MCQ2HZFFRPT2QLQMO5SFANCNFSM4I4KKDEA.

[yeswzc]

Thanks a lot.