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Old 05-12-2016, 11:46 AM   #1
SkinFlayer
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Location: Burlington, VT

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Default ViralFusionSeq Confusion

Hello everyone,

I am trying to using ViralFusionSeq to discover viral integration events in various types of sequencing data (both RNA and DNA-seq). I have successfully gotten the program and all of its dependencies installed and configured, but am running into some difficulty in adapting it from the example data to function with our own. Specifically, I'm a bit at a loss when it comes to the Clipped Sequence and Mapped Sequence keywords, and the Viral ORF's for the RP method. The trouble is that I am hoping to run the program against a full viral database rather than against a single viral sequence. I had initially hoped the change would be as simple as removing these sections from the config file, but this causes the program to fail outright as soon as it reaches the Clipped Seq module.

In short, is there a way to get VFS to search through a database automatically rather than having to explicitly pass each virus of interest as a parameter (not feasible when talking about thousands to hundreds of thousands of viruses)? Any assistance or advice would be greatly appreciated.

Sincerely,
Jason Kost
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Old 06-28-2016, 04:08 PM   #2
marcowanger
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Location: Hong Kong

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Default

Hi Jason,

Thanks for your interest in using ViralFusionSeq and I apologize that you could not run stock VFS against a whole virus database.

I am currently occupied in other projects so I could not modify the sourcecode in person. In your situtation, I would suggest writing a script to map your reads onto your viral database and extract those Reference_name you would like to analyze and input those as keywords. Having said that, you might remove those specific keywords from the example config files and leave "virus" there, which should works.
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