outputDirName
├── logs
├── LICENCE.txt
├── result
│   ├── analysisDir: Final output directory
          ├── *.merged.sorted_CGcontext.CGmap: Output after restring extracting the CG context from CGmap file (*.merged.sorted.CGmap.gz)
          ├── *.merged.sorted_CGcontext_updated.CGmap: Output after merging the asymitrical CpG's from the CGmap file (*.merged.sorted_CGcontext.CGmap)
          ├── *.merged.sorted_CGcontext_updated.CGmap: Output after merging the asymitrical CpG's from the CGmap file (*.merged.sorted_CGcontext.CGmap)
          ├── *.merged.sorted_CGcontext_putative_icr.txt: Output after scanning ICR hotspot from the updated CGmap file (*.merged.sorted_CGcontext_updated.CGmap)
          ├── *.merged.sorted_CGcontext_putative_icr.bed: htospot Converted to bed format
          ├── bed_merge_bedfile.bed: Merged all bed files from multiple tissue for downstream analysis
          ├── bed_union_bedfile.bed: Union of bed fils from multiple tissue
          ├── bedfile_putative_ICR_AllTissues.bed: Final putative ICR files that will be used to intersect with oocyte and sperm calls.
│   └── bboxinout.py
│   └── rawData: Symbolic link to your input directory
│   └── trimFastq: Directory that contain intermediate quality trimmed files and alignment bam files
        │   └── *_trimmed.fq.gz: Quality trimmed input fastq files
        │   └── *.bam: intermediate bam files
        │   └── *.merged.sorted.ATCGmap.gz: Methylation ration call for the three context from cgmaptools
        │   └── *.merged.sorted.CGmap.gz: Methylation ration call as CGmap format from cgmaptools