Can I integrate my own scRNA-seq data and bulk ATAC-seq data?

[13021969200]

Dear author:

I have a few samples of single-cell RNA and bulk ATAC sequencing data, can I integrate my own data through Dictys?

Besides, the samples were from acute myeloid leukemia patients, and there were tumor cells in the samples, can I annote tumor cells through Dictys?

Thank you very much!

[lingfeiwang]

Thanks for the questions.

Dictys can infer GRNs for cells that are already annotated. You can follow https://github.com/pinellolab/dictys/issues/23#issuecomment-1641035864 for bulk ATAC-seq data.

[13021969200]

Thanks very much for your timely reply! I still want to consult that I have already annotated the cell type in my scRNA-seq data, but I can't use the cell type information migrating to my bulk ATAC-seq data. I have read the #23 (comment) for bulk ATAC-seq data, does it mean that I can use my bulk ATAC-seq peak which contains tumor cells to get the cell type through you already annotated cell type from scATAC-seq data?And through the analysis using Dictys, can I get the integrated results containing both the scRNA-seq and bulk ATAC-seq data? Thank you very much!

 小舟从此逝 江海寄余生

----- 原始邮件 ----- 发件人：Lingfei Wang @.> 收件人：pinellolab/dictys @.> 抄送人：13021969200 @.>, Author @.> 主题：Re: [pinellolab/dictys] Can I integrate my own scRNA-seq data and bulk ATAC-seq data? (Issue #46) 日期：2023年12月16日 11点53分

Thanks for the questions. Dictys can infer GRNs for cells that are already annotated. You can follow #23 (comment) for bulk ATAC-seq data.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[13021969200]

Thanks very much for your timely reply!I still want to consult that I have already annotated the cell type in my scRNA-seq data, but I can't use the cell type information migrating to my bulk ATAC-seq data. I have read the #23 (comment) for bulk ATAC-seq data, does it mean that I can use my bulk ATAC-seq peak which contains tumor cells to get the cell type through you already annotated cell type from scATAC-seq data?And through the analysis using Dictys, can I get the integrated results containing both the scRNA-seq and bulk ATAC-seq data?Thank you very much!

 小舟从此逝 江海寄余生

----- 原始邮件 ----- 发件人：Lingfei Wang @.> 收件人：pinellolab/dictys @.> 抄送人：13021969200 @.>, Author @.> 主题：Re: [pinellolab/dictys] Can I integrate my own scRNA-seq data and bulk ATAC-seq data? (Issue #46) 日期：2023年12月16日 11点53分

Thanks for the questions. Dictys can infer GRNs for cells that are already annotated. You can follow #23 (comment) for bulk ATAC-seq data.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[lingfeiwang]

Hello. Dictys does not annotate cell types. It reconstructs GRNs. You can look for other methods for integration or cell type annotation.

[13021969200]

Thanks for you timely reply, I will look for other methods for integration or cell type annotation. Thank you!

 小舟从此逝 江海寄余生

----- 原始邮件 ----- 发件人：Lingfei Wang @.> 收件人：pinellolab/dictys @.> 抄送人：13021969200 @.>, Author @.> 主题：Re: [pinellolab/dictys] Can I integrate my own scRNA-seq data and bulk ATAC-seq data? (Issue #46) 日期：2023年12月18日 12点18分

Hello. Dictys does not annotate cell types. It reconstructs GRNs. You can look for other methods for integration or cell type annotation.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>