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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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cycle view #47

Open eesiribloom opened 7 months ago

eesiribloom commented 7 months ago

If I have files output from AA and AC, is there a way for me to experiment with the cycle view /genome browser to investigate potential larger structures formed from my cycles/paths? Would be good if I could do this without rerunning AC online. There isn't much information of this function beyond a brief mention of it on the README.

jluebeck commented 7 months ago

Hi,

Unfortunately, this technique for manual combinations of paths/cycles mentioned in the AA README is now deprecated. We are a very small team working on this tool and we did not have the bandwidth to maintain that aspect. Personally, I did not find the utility all that helpful in deciphering larger-scale ecDNA structures, and also it presented a bit of a challenge as manually piecing together ecDNA structures is not a very reproducible way to do assembly, but I suppose mileage will vary from sample-to-sample.

Generally, our thinking is that currently the most reliable way to validate large-scale genome structures of ecDNA is to perform either long-range sequence analysis (e.g. Nanopore or Bionano), or utilize an ecDNA-specific targeted sequencing assay such as CRISPR-CATCH.

I would be happy to take a look at your AA outputs if you would like some additional feedback on the sample. If the AA amplicon seems to only contain one single focal amplification, not a combination of different ecDNAs or other amplified features, then the CAMPER.py script in AmpliconSuite-pipeline's scripts/ directory can help brute-force solve the longest cyclic path.

Thanks, Jens