Several contigs hit the same species with viralComplete : which contigs should I use to map the reads with bowtie2?

Question

[bioAddict]

Hi Everyone,

I assembled RNAseq reads for my viral metagenomics study. But after the analysis of the contigs yielded with viralverify and viralcomplete, I noticed that some contigs hit the same virus species. Could you please explain me how I should handle this contigs in order construct an index with bowtie2, to map the reads and compute the coverage of each virus specie.

Thanks in advance,

[andres.firrincieli]

Hi,

I noticed that some contigs hit the same virus species. Could you please explain me how I should handle this contigs in order construct an index with bowtie2, to map the reads and compute the coverage of each virus specie.

Maybe I do not understand but, why this should be a problem?

[bioAddict]

I'm newbie in metagenomics. So I do not really understand also. That's why I asked the question. Could you please help me?

[andres.firrincieli]

You can have different contigs mapping to the same species hence, each of these contigs will contribute to the final coverage of that specie