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Old 08-02-2012, 06:21 AM   #1
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Default Viral genome assembly from RNA-seq data


I'm performing a RNA-seq analysis from a virus infected plant. After mapping the Illumina Hiseq paired reads against the plant genome, I used the unmapped reads to blast the virus genome available. Once I separated virus reads from other unmapped reads I would like to assembly the virus genome. Which is the best way to do it? I used before velvet and trinity for eukaryote transcriptome assemblies but I'm not sure if I can use the same software or approach for virus.

I would appreciate someone could guide me.

Thanks a lot
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Old 11-14-2015, 10:29 PM   #2
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generally i used bowtie first then samtools to generate mapped reads and then use Macvector software to assemble the genome.

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Old 11-15-2015, 05:21 AM   #3
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This is a very naive question, but how can you be sure that the unmapped reads belong to a virus?

Isn't it just as likely that they belong to unmapped regions of the plant transcriptome, sequencing errors, ...?
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rna-seq virus assembly

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