Super Enhancer Analysis

ROSE

Bio-Linux 에서 sudo su, (pw : manager) 관리자 모드로 들어가면 에러가 발생

# peak 파일을 gff 파일로 변환
perl peak2gff.pl MACS_peaks.xls MACS_peaks.gff

# ROSE 실행
# bam, bai 필요
# -o : output directory
python ROSE_main.py -g hg19 -i MACS2_peaks.gff -c MEC2_Input.bam -r ../mec2/MEC2K27.bam  -o rose

# annotation
# -g : hg19, hg18
# -i : input file, file name must end SuperEnhancer.table.txt
# -o : output directory
python ROSE_geneMapper.py -g hg19 -i *_SuperEnhancers.table.txt -o MEC1

Justin

분석에 필요한 파일들(아래 파일명을 반드시 사용할 것)

• MACS_peaks.xls
• MACS_peaks.narrowPeak
• input.macs_normalized.bigwig
• MACS.macs_normalized.bigwig

분석에 필요한 프로그램 설치

1. Install UCSC program http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ bigWigToBedGraph

2. BedTools https://github.com/arq5x/bedtools2/releases

3. Install R modules getopt VennDiagram

4. Make a sample file: ex) sample.conf MACS input MACS Input …

   MACS 결과파일에서 처음 시작하는 단어

   ex)
   • MACS_callpeak_on_Control.bedgraph
   • MACS_model.pdf

5. Make a length file: ex) hg19all.fa.length chr1 249250621 chr2 243199373 … The order of chromosomes should be the same as BAM files.

sudo su
manager

# Run Justin's SuperEnhancer Program
# macs : bigwig, peaks 파일이 있는 디렉토리
./macs_superenhancer hg19all.fa.length subtraction sample.txt macs

# Run Justin's annotation Program
./annotate/run_annotate ucsc/hg19ucsc.conf out_dir input_file
./run_annotate ucsc/hg19ucsc.conf out_dir input_file_1 input_file_2 ...

# bigwig subtraction
bed_op.pl -ibigwig -obigwig -l length_file -i chip.bedgraph -j input.bedgraph -op subtraction -o output.bigwig

ref

• Young Lab : http://younglab.wi.mit.edu/super_enhancer_code.html
• ROSE_main.py source https://github.com/danielsday/ROSE/blob/master/ROSE_main_turbo.py