threshold of this software to detect chimeric reads & distinguish different integration sites

[20182531027]

hi, Thanks you for the wonderful software which can analysis virus integration, and i have two questions.

firstly, when integration sites were near to each other, then it would sum to one site, so what's the minimum range to distinct different integration sites? around 500bp？
secondly, what's the percent of chimeric reads for this software to detect? we have made some attempt to discover the threshold, maybe the detectable chimeric rate is between 15%-20%
wish your kindly reply
Best wishes

[brianjohnhaas]

hi, currently, it aggregates candidates within 500 bases For min thresholds, we use 10 supporting reads, but simulations show that 5 might be sufficient. Lower than 5 and false positives accrue.

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On Sun, Dec 12, 2021 at 11:04 PM 20182531027 ***@***.***> wrote: hi, Thanks you for the wonderful software which can analysis virus integration, and i have two questions. firstly, when integration sites were near to each other, then it would sum to one site, so what's the minimum range to distinct different integration sites? around 500bp？ secondly, what's the percent of chimeric reads for this software to detect? we have made some attempt to discover the threshold, maybe between 15%-20% to distinct "split reads". wish your kindly reply Best wishes — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#39>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX5PFQL5ZO6LRWERBNLUQVWEDANCNFSM5J5EGTWA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[20182531027]

thanks for your timely reply, i wonder if i can change the parameter"500bp" , for that hpv(human papilloma viruses ) genome is small, only around 7000bp, thus 500bp seems to be a little bit broad, can the software output all the possible split sites in virus( how can i change the setting of parameter? ), while this parameter still can be applied to human genome?

[brianjohnhaas]

good point. I'll look into this. Please keep this issue open and I'll respond with updates later.

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On Tue, Dec 14, 2021 at 4:09 AM 20182531027 ***@***.***> wrote: thanks for your timely reply, i wonder if i can change the parameter"500bp" , for that hpv genome is small, 500bp seems to be a little bit broad, can the software output all the possible split sites in virus, while this parameter still can be applied to human genome? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#39 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX6CFJMYSUJSZLCNECLUQ4CTTANCNFSM5J5EGTWA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[brianjohnhaas]

aim for next release