Determining Site Of Integration Of Viral Genome Into The Host
Entering edit mode
7.7 years ago

I have paired end data for normal as well as tumour samples for cervical cancer. I am looking into the problem of determining the presence of Viral genomes [one or multiple] and their site of integration.

Determining the presence is trivial, since you can just separate out the reads unmpaaed to human genome and then re-align with the custom viral genome fasta.

I went through the question and the solutions here : Method to identify viral integration site in human genome from NGS data? but they do not solve my problem.

I came across another paper which addresses the same problem : In the 10th page they mention about using a clustering method to determine the site of integration, but I didn't quite follow the approach.

Another thing bwa-sw [as mentioned in the other biostar question] would not help me determine the integration sites, or am I mistaken ? Can someone guide me to a better approach or provide an explanation to the paper' algorithm?

ngs bwa clustering alignment bowtie2 • 3.0k views
Entering edit mode
7.7 years ago
Cacau ▴ 490

I think the following two papers are good resources. Also, in the list here ( you can find some software that are already available.

Entering edit mode
7.4 years ago
Marco Li • 0

perhaps you may try this as well.


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