How would I find out if a viral gene has been integrated into a sequence?

Question

[idkwhy90]

I am trying to determine if a patient population has integrated HPV into their genome by looking at presence of certain gene sequences. The data is from the TCGA website, which come in BAM files, so I was thinking of doing HTSeq-Count to get the counts, and then mapping the sequences that are counted back to the HPV genome. I'm not sure if this would work, however, and the BAM files from TCGA are both mapped and unmapped reads.

Any guidance? Thanks.

[GenoMax]

which come in BAM files, so I was thinking of doing HTSeq-Count to get the counts, and then mapping the sequences that are counted back to the HPV genome

You would have to convert BAM files back to fastq and then remap the reads to HPV alone or HPV+Human genome to be safe. You can then use counting program to get the counts.