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morrislab / qapa

RNA-seq Quantification of Alternative Polyadenylation
GNU General Public License v3.0
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hi, I want to know how to use this to calculate 3' RNAseq data? #1

Closed DawnEve closed 6 years ago

DawnEve commented 6 years ago

we have some scRNA-seq data from C1 system. Mapping plot shows it's a kind of 3' end RNA seq.

how to process these data, i couldn't quit know these info even after reading your paper and readme on github.

I'm a newbie about APA, would u mind to show me more clearly? Thank you.

George.

quaidmorris commented 6 years ago

Hi, Thanks for your interest in QAPA. I'm sorry, we are unable to provide this type of assistance. You may be able to find the help that you need on https://www.biostars.org/.

Best, Quaid.

Quaid Morris, PhD Associate Professor, The Donnelly Centre Departments of Molecular Genetics and Computer Science 160 College St, Rm 616 Toronto ON, M5S 3E1 Canada http://morrislab.ca http://morrislab.med.utoronto.ca cell: (416) 220 5796

On Sat, Apr 14, 2018 at 12:42 AM, DawnEve notifications@github.com wrote:

we have some scRNA-seq data from C1 system. Mapping plot shows it's a kind of 3' end RNA seq.

how to process these data, i couldn't quit know these info even after reading your paper and readme on github.

I'm a newbie about APA, would u mind to show me more clearly? Thank you.

George.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/morrislab/qapa/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AFGUdh5IPgdp5EkXqvXLXlpUDj-zV21jks5toMBpgaJpZM4TTnt1 .

DawnEve commented 6 years ago

This means QAPA cannot solve APA on 3' end RNAseq data from C1 system?

I'll try other packages then.

Thank you.

quaidmorris commented 6 years ago

Did you read the paper? The focus of QAPA is on normal RNA-seq data, not 3' end seq.

Quaid Morris, PhD Associate Professor, The Donnelly Centre Departments of Molecular Genetics and Computer Science 160 College St, Rm 616 Toronto ON, M5S 3E1 Canada http://morrislab.ca http://morrislab.med.utoronto.ca cell: (416) 220 5796

On Tue, Apr 17, 2018 at 12:34 AM, DawnEve notifications@github.com wrote:

This means QAPA cannot solve APA on 3' end RNAseq data from C1 system?

I'll try other packages then.

Thank you.

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kcha commented 6 years ago

Hi George,

Unfortunately QAPA doesn't support scRNA-seq platforms at this time.

Kevin

DawnEve commented 6 years ago

@quaidmorris I have read thoroughly as I have mentioned. At the topleft of page 13 on your paper, there is a quarter of page talking about processing 3' end data, but I still think it's a bit vague as I'm new in this area. I thought it was part of QAPA's function.

@kcha Hi, I think it is not a matter of sc or not. If the tool is effitient enough on bulk seq data, it may be used in sc seq data. Just my opinion.