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JunyueC / sci-CAR_analysis

Scripts for processing sci-RNA-seq/sci-ATAC-seq/sci-CAR reads processing
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A549 ATAC-seq Analysis #1

Open danielee0707 opened 5 years ago

danielee0707 commented 5 years ago

Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure was similar to Cicero pipeline other than some parameters. I tried doing that but couldn't produce similar tSNE results, and the plot shows that all cells are mixed together randomly and evenly when labelled with hours. I just want to ask that do the datasets downloaded from GEO (GSE117089) have columns and rows matched in order with the sparse matrix? Thanks a lot!

JunyueC commented 5 years ago

Hi Li,

Yes, it has matched rows and columns.

Attached please see the R notebook I used to process the scATAC-seq data. Different monocle versions may give slightly different result but the separation between different treatment should be clear. Please let me know if it is still not working.

Best, Jun

On Oct 11, 2018, at 8:07 PM, Chen Li notifications@github.com wrote:

Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure was similar to Cicero pipeline other than some parameters. I tried doing that but couldn't produce similar tSNE results, and the plot shows that all cells are mixed together randomly and evenly when labelled with hours. I just want to ask that do the datasets downloaded from GEO (GSE117089) have columns and rows matched in order with the sparse matrix? Thanks a lot!

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danielee0707 commented 5 years ago

Thanks for replying! I'm sorry but which notebook are you referring to? I don't see it.

JunyueC commented 5 years ago

Reattached is the notebook htm file - can you see it?

Jun

On Oct 11, 2018, at 10:56 PM, Chen Li notifications@github.com wrote:

Thanks for replying! I'm sorry but which notebook are you referring to? I don't see it.

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danielee0707 commented 5 years ago

I still see nothing. It looks like this. screenshot_20181012_113218

JunyueC commented 5 years ago

weird - it is attached on my side:

Maybe this relates with the Github mail system - can you give me your normal email and I can sent this directly to you..

Jun

On Oct 12, 2018, at 11:34 AM, Chen Li notifications@github.com wrote:

I still see nothing. It looks like this. https://user-images.githubusercontent.com/25728357/46887469-8a4f8300-ce12-11e8-9cd9-a50239295052.png — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/JunyueC/sci-CAR_analysis/issues/1#issuecomment-429419413, or mute the thread https://github.com/notifications/unsubscribe-auth/AOQeuNyJJm5qj1mJeOEDE_Rdq8wj_95nks5ukOC0gaJpZM4XYtiz.

ghost commented 5 years ago

Hi Jun, beautiful work! I also wanted to reproduce your nice monocle data. Could you send me a copy of the R notebook? my email is: hjwuwebmail@gmail.com many thanks, Jia

Duuudude commented 5 years ago

Dear Dr. Cao, I met with the same problem. I don't understand the structure of count table downloaded from GEO (GSE117089). Could you please share with me the R notebook you used to process the scATAC-seq data? My email is yibboo@outlook.com. Thank you!

Best, Yibo

Li-Xinqi commented 4 years ago

Hi, Dr.Cao, I had the same problem with Yibo. Could you please send me a copy of the R notebook? Thanks very much! My email is lxq19@mails.tsinghua.edu.cn . Xinqi

JunyueC commented 4 years ago

Sure - it is sent out

On Jan 7, 2020, at 3:20 AM, Linzy-Li notifications@github.com wrote:

Hi, Dr.Cao, I had the same problem with Yibo. Could you please send me a copy of the R notebook? Thanks very much! My email is lxq19@mails.tsinghua.edu.cn mailto:lxq19@mails.tsinghua.edu.cn . Xinqi

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rojinsafavi commented 4 years ago

Dear Dr. Cao, I was wondering if you can send me the Notebook as well? email: rsafavi@ucsc.edu

Thank you very much

YingxinLin commented 3 years ago

Dear Dr. Cao,

I had met a similar problem mentioned above when running Cicero on sci-CAR data. It would be great if you could share the R notebook for the analysis with me as well. My email is: yingxin.lin@sydney.edu.au

Thank you in advance!

Best, Yingxin

JunyueC commented 3 years ago

Sure - attached please see the R notebook for sci-ATAC-seq analysis. Please let me know in case of any questions.

On Aug 26, 2020, at 3:12 AM, Yingxin Lin notifications@github.com wrote:

Dear Dr. Cao,

I had met a similar problem mentioned above when running Cicero on sci-CAR data. It would be great if you could share the R notebook for the analysis with me as well. My email is: yingxin.lin@sydney.edu.au mailto:yingxin.lin@sydney.edu.au Thank you in advance!

Best, Yingxin

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alirezaomidi commented 3 years ago

Dear Dr. Cao @JunyueC,

I was wondering if you can send me the Notebook as well? email: aomidi@ce.sharif.edu

Best, Alireza

pronoykanti commented 1 year ago

Dear Dr. Cao, can you please send the notebook to me as well? My mail id is mondalpr@msu.edu .

Thank you. Pronoy

ianutin commented 14 hours ago

Dear Dr. Cao @JunyueC,

I was wondering if you can send me the Notebook as well? email: 547105742@qq.com

Best, Sony

ianutin commented 14 hours ago

Dear Dr. Cao, can you please send the notebook to me as well? My mail id is mondalpr@msu.edu .

Thank you. Pronoy

Dear, Pronoy Have you received this script? IF you have, could you please share me one? My email is 547105742@qq.com.

ianutin commented 13 hours ago

Thanks for replying! I'm sorry but which notebook are you referring to? I don't see it.

hello, could you please share me the script? thanks very much. my email is 547105742@qq.com. best, sony.