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WGLab / VirTect

Detection of viruses from RNA-Seq on human samples
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Start with unmapped human reads #7

Open MjelleLab opened 3 years ago

MjelleLab commented 3 years ago

Hi, I wonder if it's possible to start the analysis using reads for which those that map to the human genome are removed. For instance the unmapped output from STAR aligner using the human genome.

Best,

AtlasCUMC commented 3 years ago

Hi, For this type of task, we will need to update VirTect since the current VirTect version is not suitable for it.

Atlas.

Atlas Khan, M.Sc., M.Phil, PhD

Department of Medicine Division of Nephrology Columbia University Medical Center (CUMC), New York, USA atlas.akhan@gmail.com ak4046@cumc.columbia.edu Tel: 212-851-5216

On Fri, Nov 6, 2020 at 7:52 AM MjelleLab notifications@github.com wrote:

Hi, I wonder if it's possible to start the analysis using reads for which those that map to the human genome are removed. For instance the unmapped output from STAR aligner using the human genome.

Best,

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MjelleLab commented 3 years ago

Hi, is there any way of updating the software to allow unmapped human reads as input?

MjelleLab commented 3 years ago

Is there any problem using unmapped reads as input and start by mapping them again to the genome? It will just be a second round of mapping and should not affect the results?

AtlasCUMC commented 3 years ago

Should be fine to re-aligned....

Atlas Khan, M.Sc., M.Phil, PhD

Department of Medicine Division of Nephrology Columbia University Medical Center (CUMC), New York, USA @. @. Tel: 212-851-5216

On Sun, May 9, 2021 at 2:57 PM MjelleLab @.***> wrote:

Is there any problem using unmapped reads as input and start by mapping them again to the genome? It will just be a second round of mapping and should not affect the results?

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