Once you have detected circular DNA in your samples you will probably be interested at looking at the output files. Tutorial: identification of repetitive circular DNA using Circle Map Repeats Tutorial: identification of mappable circular DNA using Circle Map Realign In the wiki, you can try and learn using Circle-Map with the following tutorials: We have created a Circle-Map wiki that explains step by step how you can go from your raw sequencing reads to interpretable results. Now you are ready to get started detecting circular DNA.
#CIRCLE BED INSTALL#
Note: If you want to simulate circular DNA short reads, you will need to install BBMap and ART on your system. This will install Circle-Map, and all the external packages required to run every part of Circle-Map software. Getting started InstallationĬircle-Map runs on GNU/Linux operating systems, requires >=python3.6 and can be installed and set-up using the following ways: In our recent paper ( ) we show how this approach dramatically increases sensitivity while retaining high precision. Which allows for a more accurate detection of the circular DNA breakpoints. 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. In this cases, the aligner will report a read alignment containing some of the bases unmapped (e.g soft-clipped reads). 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. split reads) to detect genomic rearrangements supporting a circular DNA structure. 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.
Why should I use Circle-Map?Ĭircle-Map takes as input an alignment of reads to a reference genome (e.g. The package contains easy to run algorithms to accurately detect circular DNA formed from mappable and non mappable regions of a genome. Welcome to Circle-Map official repository!Ĭircle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles.
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