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AmpliconSuite / AmpliconClassifier

Classify output of AmpliconArchitect to detect types of focal amplifications present
BSD 2-Clause "Simplified" License
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Can AmpliconClassifier output the classification of each Cycle in the "*_amplicon_cycles.txt" file? #2

Closed kerenzhou062 closed 3 years ago

kerenzhou062 commented 3 years ago

Hi Jens,

Can you make AmpliconClassifier output the classification of each Cycle in the "*_amplicon_cycles.txt" file?

Best, Keren

jluebeck commented 3 years ago

Hi Keren,

I will certainly consider this. Perhaps something that writes a new cycles file including annotations about whether each path/cycle conforms to ecDNA-like, BFB-like, or other. Is this what you had in mind?

Best, Jens

On Tue, Oct 20, 2020 at 3:02 PM Keren Chow notifications@github.com wrote:

Hi Jens,

Can you make AmpliconClassifier output the classification of each Cycle in the "*_amplicon_cycles.txt" file?

Best, Keren

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kerenzhou062 commented 3 years ago

Hi Jens,

Yes, that's what I had in mind. It can be written in the new annotation file and the format may be just like bellow:

Cycle=1;Copy_count=#float;Class=circular Cycle=2;Copy_count=#float;Class=BFB-like

Of course, you can do it in your own way.

Thanks, Keren

kerenzhou062 commented 3 years ago

Hi Jens,

When will this new functionality of AmpliconClassifier be available for download?

Best, Keren

jluebeck commented 3 years ago

Hi Keren,

Apologies, but I have not had time to work on this specific feature. I'd also draw your attention to --report_genes flag, which will output a bed file of the ecDNA (or BFB) regions of the AA amplicons which are predicted to contain ecDNA. While it does not tag specific cycles as ecDNA-like, you can determine which regions contain ecDNA-like cycles.

Best regards, Jens

kerenzhou062 commented 3 years ago

Hi Keren,

Apologies, but I have not had time to work on this specific feature. I'd also draw your attention to --report_genes flag, which will output a bed file of the ecDNA (or BFB) regions of the AA amplicons which are predicted to contain ecDNA. While it does not tag specific cycles as ecDNA-like, you can determine which regions contain ecDNA-like cycles.

Best regards, Jens

Hi Jens,

I've checked the results from --report_genes, but it does not really feed my needs. Could you please develop this feature sooner or later? It'll really help a lot on my present project.

Thanks! Keren

jluebeck commented 3 years ago

Hi Keren,

I have added a feature which will annotate the cycles file. It creates a new cycles file, which contains some annotations about size, classification type, etc. of the amplicon. You can do --annotate_cycles_file to turn it on when you run AC.

Best, Jens

kerenzhou062 commented 3 years ago

Hi Keren,

I have added a feature which will annotate the cycles file. It creates a new cycles file, which contains some annotations about size, classification type, etc. of the amplicon. You can do --annotate_cycles_file to turn it on when you run AC.

Best, Jens

Hi Jens,

I've tried this new feature, and that's what I want!

Thank you so much!

Best, Keren