Pipeline to identify candidate circular regions in Circle-seq short-read paired-end sequecing data. Developed by Richard Koche, adapted to BIH cluster by @haasek and maintained by @madagiurgiu25.
- Installation
- Usage
- Run circle-enrich-filter example
- Run circle-enrich-filter with PDX data
- Citation
- License
Prequisites are conda and pgltools v2.2.0. Compatible with python 2.7 and python 3.7.
Compatible with human (GRCh38.p13, GRCh37.p13, hs37d5, hg38, hg19) and mouse (GRCm38) genome assemblies.
Choose one of the python versions to install the conda environment.
Use circleEnrich_env.yml to download and install the following dependencies:
- bedtools=2.29.2
- deeptools=3.1.3
- homer=4.11
- openjdk=11.0.1
- picard=2.22.8
- python=2.7.15
# create conda environment
git clone https://github.com/henssen-lab/circle-enrich-filter.git
cd circle-enrich-filter
mamba env create -f circleEnrich_env.yml
Use circleEnrich_env_py37.yml to download and install the following dependencies:
- python==3.7
- bedtools==2.30.0
- picard==2.27.5
- samtools==1.16
- openjdk==11.0.15
- homer==4.11
- deeptools==3.5.1
# create conda environment
git clone https://github.com/henssen-lab/circle-enrich-filter.git
cd circle-enrich-filter
mamba env create -f circleEnrich_env_py37.yml
git clone https://github.com/billgreenwald/pgltools.git
# use the v2.2.0 version
export PATH=$PWD/pgltools/sh:$PATH
The tool requires as input mapped reads.
Usage: bash run_CircleEnrichFilter.sh [OPTION..] -i <reads.bam> -o <outdir>
circle-enrich-filter version 1.0.0
Find enriched regions from Circle-seq paired-end short-read sequencing data.
Options:
-i Input bam file.
-o Output directory.
-s Number of circle-supporting (split and/or outward facing) reads at edge of each putative circle (default=2)
-m Number of bp for initial enriched region merging; based on tests in neuroblastoma data
-@ Number of threads (default=4)
-h Help
-V Print program version
Run test example using the 2:14508020-18508849 region from CHP212 human cellline sequenced using the Circle-seq Illumina sequencing.
bash run_CircleEnrichFilter.sh -i example/output/chp212_2_14508020_18508849.bam -o example/2_14508020_18508849.fa
The pipeline generates the all files under example/ouput. The final enriched regions found by circle-enrich-filter is Regions.enriched.merged.b2bRefined.Counts.ThreshFinal.bed. The header is described bellow:
| column | description |
|---|---|
| 1 | reference sequence name |
| 2 | start position |
| 3 | end position |
| 4 | edge counts (split-reads spanning the junction) |
| 5 | all counts (coverage all reads spanning the junction) |
In case you run PDX samples, please consider annotating all chromosomes from the mouse using m.*, .e.g m.1 or m.chr1.
Koche, R.P., Rodriguez-Fos, E., Helmsauer, K. et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 52, 29-34 (2020). https://doi.org/10.1038/s41588-019-0547-z
Circle-enrich-filter is distributed under the GNU General Public License v3.0. Consult the accompanying LICENSE file for more details.