Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. Circular DNA (also called eccDNA,ecDNA,circDNA...) have recently gained quite attention due to their role in cancer as a mutational process in eukaryotic genomes.The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome.
Why should I use Circle-Map:
Circle-Map takes as input an alignment of reads to a reference genome (e.g. a BWA-MEM generated BAM file) and like other methods, it will use those alignments to detect cases were the read has been split into two segments (e.g. split reads) to detect genomic rearrangements supporting a circular DNA structure.
However, this approach results in many split read alignments being missed because the aligner is not able to map both split segments of the read, either because they are too short or because they align to too many places. In this cases, the aligner will report a read alignment containing some of the bases unmapped (e.g soft-clipped reads).
Unlike other methods, Circle-Map is able to map both segments of the soft-clipped reads by realigning the unmapped parts probabilistically to a graph representation of the circular DNA breakpoints. Which allows for a more accurate detection of the circular DNA breakpoints. In our recent preprint (https://www.biorxiv.org/content/10.1101/654194v1) we show how this approach dramatically increases sensitivity while retaining high precision.
Feedback is more than welcome!
Please let me know, why it is still not working with me? below is the pipeline and the error shows when I entered the pipeline.
I have post an answer in the other thread