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after running AA and AC,I konw I got some amplication with eccDNA. However, in fact, a cycle defined in one amplicon of AA may contain multiple segments. However, when we run Circle-Map on CIRCLE-seq …
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After running Circle-map, I can get a bed file of ECC locations. But how can I get the ECC reads? I think not all reads that in the ECC locations are ECC reads.
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Can you help me understand the principle of `convert_cycles_file.py`? I found after running this script, my orignal cycle have more segments in it. and I don't know why. for example:
my raw cycle f…
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Hello iprada,
I have tried CIRCexplorer2 to detect eccDNA as mentioned in your paper, but I got few eccDNA output. I guess I misused the command of CIRCexplorer2. Could you please tell me the detail …
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Hello,
I installed Circle-Map via conda and encountered the following problem:
```
Computing the coverage of the identified eccDNA
Merging intervals for coverage computation
Traceback (most r…
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Hello,
Thanks for sharing this pipeline! I am all set up but I'm not sure how to go forward on this as I see from the example that only two fastq files need to be specified whereas in my 10x scATAC…
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Hi all,
Looking at one cluster plot:
![image](https://user-images.githubusercontent.com/53702866/97319141-81e50c00-1864-11eb-8dfb-6503b0b73bb1.png)
This I think represents chromothripsis. Do yo…
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## Version of Singularity:
2.5.2-dist
### Expected behavior
singularity exec cider.simg eccDNA.py
Usage: cs-eccDNA.py [OPTIONS] LIST_FILE GENOME_FILE
Try "cs-eccDNA.py --help" for help.
…
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editor preferred term: Circulome-seq
alternate terms: eccDNA-seq, extrachromosomal circular DNA sequencing assay
textual definition: An assay which aims at identifying the endogenous population of e…