Version:
nf-core/circrna v0.0.1dev
Branch:
https://github.com/nf-core/circrna/tree/new_benchmarking
After all four runs of nf-core/circrna on both data types of both datasets,
move the pipeline output of the BJS detection (bsj_detection) into eiter polya/bed, or total/bed, based on
what datatype and dataset was used. Make sure the pipeline was executed using the blacklist.
Extract bam files located in tools/unified/start/2nd_pass into a shared directory polya/bam or total/bam
based on datatype and dataset.
The data directory structure should then be:
data
├── blacklist
│ └── hg38-blacklist.v2.bed
├── DEEP
│ ├── polya
│ │ ├── bam
│ │ │ ├── 1_polyA_41_Hf01_LiHe_L005.Aligned.out.bam
│ │ │ └── ...
│ │ ├── bed
│ │ │ ├── circexplorer2
│ │ │ │ ├── blacklist
│ │ │ │ │ ├── 1_polyA_41_Hf01_LiHe_L005.circexplorer2.blacklist.bed
│ │ │ │ │ └── ...
│ │ │ ├── ciriquant
│ │ │ │ ├── blacklist
│ │ │ │ │ ├── 1_polyA_41_Hf01_LiHe_L005.ciriquant.blacklist.bed
│ │ │ │ │ └── ...
│ │ │ ├── dcc
│ │ │ │ ├── blacklist
│ │ │ │ │ ├── 1_polyA_41_Hf01_LiHe_L005.dcc.blacklist.bed
│ │ │ │ │ └── ...
│ │ │ ├── find_circ
│ │ │ │ ├── blacklist
│ │ │ │ │ ├── 1_polyA_41_Hf01_LiHe_L005.find_circ.blacklist.bed
│ │ │ │ │ └── ...
│ │ │ └── segemehl
│ │ │ ├── blacklist
│ │ │ │ ├── ...
│ │ │ │ └── 9_polyA_51_Hf04_BlEM_L002.segemehl.unified.blacklist.bed
│ └── total
│ ├── bed
│ │ ├── circexplorer2
│ │ │ ├── blacklist
│ │ │ │ └── 9_polyA_51_Hf04_BlEM_L002.segemehl.unified.blacklist.bed
│ │ ├── ciriquant
│ │ ├── ...
│ │ └── segemehl
├── GSE138734
│ ├── polya
│ │ └── ...
│ └── total
│ └── ...
└── rrna_gtf
└── ensembl_rRNA.gtf
Blacklist: https://github.com/Boyle-Lab/Blacklist/
Amemiya, H.M., Kundaje, A. & Boyle, A.P. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep 9, 9354 (2019). https://doi.org/10.1038/s41598-019-45839-z
rRNA GTF: https://github.com/zxl124/rRNA_gtfs
After having set up everything, run
cd src/
bash run_analysis.sh