Data/WGSinferredCircles_eccDNA.txt has some very large fragments

[shaka-emperor]

Hi, I have read your impressive work "Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma Nat Genet (2020)." But I didn't find some explicit criteria to distinguish ecDNA and eccDNA in this paper, like how many bases, etc. Then I look up "Data/WGSinferredCircles_eccDNA.txt", and "Data/WGSinferredCircles_ecDNA.txt". However, the result confuses me a lot....... eccDNAs contain some really big fragments, and ecDNAs contain some tiny fragments......

awk '{print $3-$2}' WGSinferredCircles_ecDNA.txt | sort -n | wc -l
awk '{print $3-$2}' WGSinferredCircles_eccDNA.txt | sort -n | wc -l

[henssenlab]

Please contact ***@***.*** for questions regarding the code. Thank you Anton Henssen

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On Sun, Sep 5, 2021 at 2:45 PM shaka-emperor ***@***.***> wrote: Hi, I have read your impressive work "Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma Nat Genet (2020)." But I didn't find some explicit criteria to distinguish ecDNA and eccDNA in this paper, like how many bases, etc. Then I look up "Data/WGSinferredCircles_eccDNA.txt", and "Data/WGSinferredCircles_ecDNA.txt". However, the result confuses me a lot....... eccDNAs contain some really big fragments, and ecDNAs contain some tiny fragments...... awk '{print $3-$2}' WGSinferredCircles_ecDNA.txt | sort -n | wc -l awk '{print $3-$2}' WGSinferredCircles_eccDNA.txt | sort -n | wc -l — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALJJIWQOBFH3ESMYUO5MXA3UANQ7FANCNFSM5DOY52MQ> . 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>.

[shaka-emperor]

The email address is masked...I cannot get it