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WGLab / VirTect

Detection of viruses from RNA-Seq on human samples
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VirTect on dog genome #2

Open DianaG86 opened 5 years ago

DianaG86 commented 5 years ago

Hello, is it possible to run VirTect on non-human genomes? I'd like to try it on dog genome. Thank you very much. Diana

AtlasCUMC commented 5 years ago

Hi @Diana, Thank you for your email. For now VirTect only working with human samples, however in our future version, we may include other species such as dog etc.

Atlas Khan (PhD)

Department of Medicine (Division of Nephrology), Columbia University Medical Center (CUMC), New York, USA.

On Wed, Jul 3, 2019 at 5:20 AM DianaG86 notifications@github.com wrote:

Hello, is it possible to run VirTect on non-human genomes? I'd like to try it on dog genome. Thank you very much. Diana

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DianaG86 commented 5 years ago

Thank you for your prompt reply!

Diana

Diana Giannuzzi, DVM, PhD Student Dept. of Comparative Biomedicine and Food Science University of Padua - Veterinary Medicine AGRIPOLIS - viale dell'Università, 16 35020 Legnaro (PD) - Italy Tel.: +39 049 8272518

Il giorno mer 3 lug 2019 alle ore 15:07 Atlas Khan notifications@github.com ha scritto:

Hi @Diana, Thank you for your email. For now VirTect only working with human samples, however in our future version, we may include other species such as dog etc.

Atlas Khan (PhD)

Department of Medicine (Division of Nephrology), Columbia University Medical Center (CUMC), New York, USA.

On Wed, Jul 3, 2019 at 5:20 AM DianaG86 notifications@github.com wrote:

Hello, is it possible to run VirTect on non-human genomes? I'd like to try it on dog genome. Thank you very much. Diana

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/WGLab/VirTect/issues/2?email_source=notifications&email_token=AES4WPRK6WSA4ZMHGCQQMCTP5RVNFA5CNFSM4H5DWT62YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G5CS6MQ , or mute the thread < https://github.com/notifications/unsubscribe-auth/AES4WPQOJPA3VI2HD7IG3SDP5RVNFANCNFSM4H5DWT6Q

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Saurav-g-hub commented 2 years ago

Hello Diana,

I am trying to run VirTect or any other software that would run for non human samples. Have you tried some software which were successfull. Can you suggest some softwares that may be helpful in non human samples.

Thank you

Saurav

Saurav-g-hub commented 2 years ago

Hi Altas,

I am curious to know that what may be the possible reasons behind VirTect only working with human samples. Can you provide some details so that it can be tailored for other vertbrates having different number of chromosomes. It will be really helpful if you can provide some solution.

Thank you

Regards, Saurav Mandal, PhD

DianaG86 commented 2 years ago

Hi Saurav, I’ve finally used virusfinder2. All the others had a lot of troubles when I tried to use them! Best, Diana

Il giorno gio 16 dic 2021 alle 07:23 Saurav Mandal @.***> ha scritto:

Hello Diana,

I am trying to run VirTect or any other software that would run for non human samples. Have you tried some software which were successfull. Can you suggest some softwares that may be helpful in non human samples.

Thank you

Saurav

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Saurav-g-hub commented 2 years ago

Hi Diana, Thank you so much for quick response. We have tried virusfinder2 as well but in step3 of virus_detection part using SVDetect it is not able to generate the results-virus-loci.txt file. The results-virus-list.txt gets generated tough. We are particularly intersted in viral integration loci. I have few more questions,

  1. Did you used the required software versions for virusfinder2 as mentioned in their manual. Like did you used other samtools versions instead of samtools 0.1.18 as mentioned.
  2. Were you able to generate the results-virus-loci.txt file for dog genome.
  3. Also, did you made any changes in the virusfinder2 perl code(or SVDetect or anywhere else) or used conda environment to execute the software completely.

Thank you,

Best, Saurav