Comments (10)
Hi,
Could you elaborate a bit more?
Do you wanna get the read counts for every ecDNA in your sample? If so, do you program in python?
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exactly, I wanna get the read counts for every ecDNA in my sample, but I don't know how to do it...
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Do you program in python?
from circle-map.
sorry... I only know it's a programming language. if it helps, I'd love to learn it
from circle-map.
If you program in python, you could use pysam (https://pysam.readthedocs.io/en/latest/api.html) to get the counts. I also thing that "bedtools coverage" does exactly what you want. If you do not know what I am talking about, I encourage you to find some bioinformatics collaborator that could help you.
Best,
Iñigo
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Thanks a lot~~~ these clues are really valuable ~~~
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You are very welcome.
Sorry I cannot be more helpful. I am finishing my PhD and I am quite busy. Feel free to open a new issue if you have more questions
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Dear iprada
Hi, I used bedtools coverage to get read counts for a specific ecDNA. But how to use these reads to trace back the copy number of a specific ecDNA?
Besides, is it appropriate to directly use Circle-Map realignmy_unknown_circle.bed file (split reads + discordant reads, or just split reads) to indicate ecDNA copy number? Because my understanding is that these reads contain breakpoints. For instance, if this putative ecDNA have 5 split reads, then I can say the raw data contain 5 copies of this ecDNA?
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Hi @shaka-emperor,
This outside my scope and it heavily depends on your experimental setting. If you do not have anybody with a rigurous statistics/quantitative bioinformatics background, I encourage you to find a collaborator that could help you there.
I am sorry I cannot help more on this.
Best,
Iñigo
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Thank you anyway, you have helped me a lot~~
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