henssenlab
commented
3 years ago Please contact @.*** for questions regarding the code. Thank you Anton Henssen
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
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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