常用软件命令

FastQC

./FastQC/fastqc -o ./chipseq/QC -t 10 case.fq

Bowtie

./miniconda3/bin/bowtie -e 70 -k 2 -n 2 -m 2 -S -q genome case.fq

./software/samtools-1.0/samtools view -Sb case.sam > case.bam

./software/samtools-1.0/samtools sort case.bam case.sort

Macs

macs14 -p 1e-9 -w -S --keep-dup=auto --wig --single-profile --space=50 -c Input.sort.bam -t STAT3.sort.bam -g hs -n test_macs

./jy/miniconda3/bin/macs2 callpeak -t Input.sort.bam -c STAT3.sort.bam -f BAM -g hs -n test -B -q 0.01

macs2 callpeak -t input_dechrM_picard.sort.bam -g hs --keep-dup all --name name_BAMPE --bdg --broad --SPMR --nomodel --extsize 200 -q 0.01

BedTools

./software/bedtools2/bin/bedtools intersect -a 2000.bed -b macs_peaks.bed -wo > TE3_control.bed

BED-process

cat gene_2000_4.bed |sed 's/"//g' > gene_2000_5.bed

awk '{gsub(" ","\t"); print $0 }' gene_2000_6.bed > gene_2000_7.bed

sed -i '1d' gene_2000_2.bed > gene_2000_7.bed

Fimo

./software/bedtools2/bin/bedtools getfasta -fi genome.fa -bed H3K27ac_peaks.bed -fo H3K27ac_peaks.fa -name

./meme_4.12.0/src/fimo -verbosity 1 -text VertebratePWMs.txt H3K27ac_CM_Rep_1_peaks.fa > fimo.txt