因子和主成分析法：ATAC-seq6
因子和主成分析法：ATAC-seq6
寻找motif构造HOMER软件指定使用的peak文件格式
mkdir ../homer
ls *.sorted.narrowPeak | while read id;
do
file=$(basename $id )
sample=${file%%.*}
echo $sample
awk '{print $4"\t"$1"\t"$2"\t"$3"\t "}' $id > ../homer/${sample}.homer_peaks_bed
findMotifsGenome.pl ../homer/${sample}.homer_peaks.bed mm10 ../homer/${sample}_motifDir -len 8 10 12
done
image.png
差异peak分析构造计数矩阵
#合并bed文件
cat 2-cell-1_peaks.narrowPeak 2-cell-2_peaks.narrowPeak 2-cell-4_peaks.narrowPeak 2-cell-5_peaks.narrowPeak | sort -k1 1 -k2 2n | bedtools merge | uniq > merge.bed
awk '{print "peak_"NR"\t"$1"\t"$2"\t"$3"\t""."}' merge.bed > merge.bed.saf
featureCounts -T 4 -a merge.bed.saf -F SAF -o counts_subread.txt ../bowtie2/*.bam
head counts_subread.txt
# Program:featureCounts v2.0.1; Command:"featureCounts" "-T" "4" "-a" "merge.bed.saf" "-F" "SAF" "-o" "counts_subread.txt" "../bowtie2/2-cell-1.bam" "../bowtie2/2-cell-2.bam" "../bowtie2/2-cell-4.bam" "../bowtie2/2-cell-5.bam"
Geneid Chr Start End Strand Length ../bowtie2/2-cell-1.bam ../bowtie2/2-cell-2.ba../bowtie2/2-cell-4.bam ../bowtie2/2-cell-5.bam
peak_1 chr1 3516001 3516332 . 332 6 10 2 30
peak_2 chr1 3661830 3662104 . 275 3 9 1 14
peak_3 chr1 3673035 3673612 . 578 16 36 5 21
peak_4 chr1 3728391 3728824 . 434 4 23 3 14
peak_5 chr1 3930572 3930989 . 418 19 21 0 24
peak_6 chr1 3958616 3959549 . 934 103 155 46 130
peak_7 chr1 4051851 4052293 . 443 7 10 0 26
peak_8 chr1 4091560 4092122 . 563 7 20 0 4
拿到表达矩阵后，后面的流程和RNA-Seq分析流程一样，用DESeq2进行差异分析。
