Can I integrate my own scRNA-seq data and bulk ATAC-seq data?
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13021969200 commented
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 commented
Thanks for the questions.
Dictys can infer GRNs for cells that are already annotated. You can follow #23 (comment) for bulk ATAC-seq data.
13021969200 commented
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 ***@***.***>
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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.
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13021969200 commented
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.
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Reply to this email directly, view it on GitHub, or unsubscribe.
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lingfeiwang commented
Hello. Dictys does not annotate cell types. It reconstructs GRNs. You can look for other methods for integration or cell type annotation.
13021969200 commented
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.
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