Interpret result

[byeongill]

Hi.
I executed exogene on WGS data. I think final output file is "integration.tsv".
I show my example output.

The results show many integration site for Encephalomyocarditis virus.
I think it is false positive because this sample is liver cancer. Perhaps HBV is true.

How filter out the false positive??
And, the results show many SOFTCLIP_MAPQ is 0%. is it ok?

Thanks.

[zstephens]

Greetings! It looks like you may be using an older version of Exogene, in the v15 version I removed a few viruses that were giving a problematic number of false positives, such as that Encephalomyocarditis virus. So you can safely ignore those. Exogene was tested primarily on HBV integrations in liver cancer samples, so I'm inclined to trust those integration sites.

That SOFTCLIP_MAPQ0 column is used to indicate how many of the supporting softclipped reads have mapping quality 0, so 0% means none of them are multimapped, so that's actually a good thing.