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I'm sorry to bother you, but I had a strange problem when using circle-map for EccDNA identification. I have a total of 14 samples, of which 12 samples were identified very quickly and finished in abo…
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Hi,
It's really interesting tool to identify circle DNA from DNAseq data. But, recently, we are considered with the variety of circle DNA length and length of insenrtion of reads, which would influen…
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Hello,
I was trying to run the pipeline with my eccDNA data. I got some confusing results. My reference (>MLV) is 8857bp, however, in the output, some fragments are longer than the reference.
For …
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v0.4.13
The coordinate in cycle file is, for example,
chr1 100 *500*
however, in the eccDNA_x_intervals.bed output file, it becomes
chr1 100 **501**
for other outputs, like BFB_x_intervals.…
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I read your code of map-sr mode, I found that you used pybedtools and pandas to process the bam2bed file and found split and discordant reads in it. So if I have a very big data, It may cause crash !
…
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Dear,
I recently read your excellent work on circle-map, thank you for your contribution, but I have some small confusion, I noticed that in the middle part of the paper you used data from Circle-seq…
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Hi Inigo,
‘’If there are the strong disagreements between the number of discordant reads and split reads the circular DNA should be handled with care. As an example, if a circular DNA contains tens…
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文献描绘的ecDNA的概念大概应该是:高度扩增的,携带有oncogenes的环状DNA ,不一定要特别大。据我了解circle-Map仅限于找到拆分的两个junction位点,请问你大概用的什么原理找的ecDNA呢
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Hi.
I have applied the program in WGS data of several cell lines. I started from .fastq files and used PrepareAA.py to generate CNV calls. However, all of these runs generated empty AA_CNV_SEEDS.bed…
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Hello
I want to know if AR supports CRAM file as input? Thanks.