[swbarnes2]

The virus transcribed because I found it when I did the alignment of the reads with the virus sequence, and when I did the Novo Assembly. Is this what you mention?

Does transcribed necessarily mean integrated?

- Generate the data base (consensus sequence) with Samtools tool

That was never going to work. Nothing in samtools is smart enough to make a reference genome by inserting a whole viral genome into a mammalian one.

De novo in theory would work, but in practice, is a huge job for a mammalian transcriptome. And are you sure that your virus in integrated such that it makes a fusion transcript? Isn't it possible that it's just hanging out in intergenic space?

Your data seems to be telling you that you have no insertions of the kind you want. Is it really so very unlikely that that's not correct?

[hmaa]

Does transcribed necessarily mean integrated?

That was never going to work. Nothing in samtools is smart enough to make a reference genome by inserting a whole viral genome into a mammalian one.

De novo in theory would work, but in practice, is a huge job for a mammalian transcriptome. And are you sure that your virus in integrated such that it makes a fusion transcript? Isn't it possible that it's just hanging out in intergenic space?

Your data seems to be telling you that you have no insertions of the kind you want. Is it really so very unlikely that that's not correct?

I don't sure where is the integration site, in intergenic space or like funsion transcritp, however by the results seems this can be in intergenic space. Like I said, I only have a experimental reference where I could find the integration site (particular position on the chromosome 2)

[hmaa]

Does transcribed necessarily mean integrated?



That was never going to work. Nothing in samtools is smart enough to make a reference genome by inserting a whole viral genome into a mammalian one.

De novo in theory would work, but in practice, is a huge job for a mammalian transcriptome. And are you sure that your virus in integrated such that it makes a fusion transcript? Isn't it possible that it's just hanging out in intergenic space?

Your data seems to be telling you that you have no insertions of the kind you want. Is it really so very unlikely that that's not correct?

About if transcribed necessarily mean integrated, this is a condition at the experiment.

[marcowanger]

About if transcribed necessarily mean integrated, this is a condition at the experiment.

You may want to try VirusSeq or VirusFusionSeq

http://seqanswers.com/wiki/VirusSeq
http://seqanswers.com/wiki/ViralFusionSeq