RE: MARATHON

[Jiang, Yuchao]

Hi,

 

Thanks for your interest. What do you mean by saying that you are stuck in 4.1.1?

 

From: Simoneaux, Tankya N <TN...@pitt.edu>
Sent: Tuesday, June 18, 2019 1:34 PM
To: Jiang, Yuchao <yuc...@email.unc.edu>
Subject: MARATHON

 

Good Afternoon,

I found your collaborative article 

MARATHON: Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny

Yuchao Jiang, Hao Chen, Gene Urrutia, Zilu Zhou, Nancy Zhang

2018-10-09

I am trying to run the example within and so far I am stuck in the 4.1.1 Codex section. I am graduate student working as intern @University of Pittsburgh and have been tasked to find a tool to analyze allele-specific copy number variations in TCGA data.

 

Could You Please advise?

I look forward to your reply!

[Jiang, Yuchao]

Hi,

Thanks for your patient and I apologize for the errors you encountered — they were due to the recent updates in CODEX2 leading to discrepancies. I’ve updated the tutorial as well as the R markdown. Please try again and feel free to let us know if you have further questions.

Yuchao

On Jun 19, 2019, at 4:22 PM, Simoneaux, Tankya N <TN...@pitt.edu> wrote:

Good Afternoon,

I have been working through all of the errors. However, I encountered one that really baffles me.

<image.png>

Could you please advise?

I will continue to try different things.

Thanks in Advance!

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From: Jiang, Yuchao <yuc...@email.unc.edu>
Sent: Tuesday, June 18, 2019 3:39 PM
To: Simoneaux, Tankya N
Subject: Re: MARATHON

 

It’s the same issue. You can remove mapp and gc from the arguments.

Sent from my iPhone

On Jun 18, 2019, at 3:31 PM, Simoneaux, Tankya N <TN...@pitt.edu> wrote:

That worked, Thanks!

My new error is about unused arguments:

<image.png>

This suppose to be QC.

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From: Jiang, Yuchao <yuc...@email.unc.edu>
Sent: Tuesday, June 18, 2019 2:26 PM
To: Simoneaux, Tankya N
Subject: RE: MARATHON

 

I will look into this but it’s due to the different functions being called. In CODEX, getbambed has a chr argument; in CODEX2, we suppressed that and retrieve that information directly from the bed input…

 

Try simply removing the chr argument?

 

From: Simoneaux, Tankya N <TN...@pitt.edu> 

Sent: Tuesday, June 18, 2019 1:47 PM
To: Jiang, Yuchao <yuc...@email.unc.edu>

Subject: Re: MARATHON

 

Stuck in this section of the pipeline (4.1.1. CODEX for data normalization and total copy number analysis in normal), my error message I pasted into the previous message.

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From: Jiang, Yuchao <yuc...@email.unc.edu>
Sent: Tuesday, June 18, 2019 1:41 PM
To: Simoneaux, Tankya N
Cc: cod...@googlegroups.com
Subject: RE: MARATHON

 

<image001.png>