search

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
300 stars 125 forks source link

FindTransferAnchors #107

Open hjack123 opened 4 years ago

hjack123 commented 4 years ago

before applying FindTransferAnchors, is the gene activity matrix being normalized?

r3fang commented 4 years ago

No it’s raw count

Sent from my iPhone

On Sep 26, 2019, at 6:15 PM, hjack123 notifications@github.com wrote:

before applying FindTransferAnchors, is the gene activity matrix being normalized?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

hjack123 commented 4 years ago

Thank you! and when making the gene/peak activity matrix, were they preselected by the promoter region?

r3fang commented 4 years ago

The peak or gene region is customized and you can choose to use any regions or promoters. The gene.bed file used in the demo are all genes. For integration, only variable genes identified using RNA seq are used for analysis.

Sent from my iPhone

On Sep 27, 2019, at 11:10 AM, hjack123 notifications@github.com wrote:

Thank you! and when making the gene/peak activity matrix, were they preselected by the promoter region?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

hjack123 commented 4 years ago

Hi, thank you so much for replying again!! Is the weight reduction also using LSI?

r3fang commented 4 years ago

No. It uses the diffusion maps

Sent from my iPhone

On Sep 27, 2019, at 2:01 PM, hjack123 notifications@github.com wrote:

Hi, thank you so much for replying again!! Is the weight reduction also using LSI?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

ahmedabbas81 commented 4 years ago

Dear all,

And how about the gene expression matrix? is it normalized before Transfer anchors or raw count?

And for gene activity matrix, which one is used (from Cicero or the simple one in Seurat tutorial)?

Thank you

ahmedabbas81 commented 4 years ago

Dear all,

And how about the gene expression matrix? is it normalized before Transfer anchors or raw count?

And for gene activity matrix, which one is used (from Cicero or the simple one in Seurat tutorial)? @hjack123 @r3fang Thank you