越哥服务器上分析流程留存

作者: pudding815 | 来源:发表于2023-09-23 14:17 被阅读0次

蝌蚪互娱|用户留存分析指南(三)：如何建立用户留存策略
用户留存分析指南(三)：如何建立用户留存策略
用户留存分析指南(二)：用户留存的三个阶段
数据分析的要点
PostgrepSQL的连接和使用
20171104-多看阅读与两个竞品的分发功能分析
留存分析
留存分析
留存分析
Clickhouse(流量分析(二).留存分析案例)

把sortbam文件全部上传到越哥服务器上
给服务器上安装了bedgraphtobw,直接用就行了
传文件使用的命令是

scp -r -P 23171 /work/home/algroup01/username/wangwenjing/wangyue_cuttag/H3K27ac/align/sortbam/ t170409@116.237.217.20:/home/data/t170409/data/wy_cuttag_project

1、合并bam

#切换wycut环境
conda activate wycut
samtools merge K27_merge_246.sort.bam H3K27ac-2.sort.bam H3K27ac-4.sort.bam H3K27ac-6.sort.bam -@25
samtools merge K27_merge_7810.sort.bam H3K27ac-7.sort.bam H3K27ac-8.sort.bam H3K27ac-10.sort.bam -@25
samtools merge PR_merge_134.sort.bam PR-1.sort.bam PR-3.sort.bam PR-4.sort.bam -@25
samtools merge PR_merge_567.sort.bam PR-5.sort.bam PR-6.sort.bam PR-7.sort.bam -@25

2、bam转bw

#bam转bedGraph
bedtools genomecov -bga -ibam K27_merge_246.sort.bam > K27_merge_246.bedGraph
bedtools genomecov -bga -ibam K27_merge_7810.sort.bam > K27_merge_7810.bedGraph
bedtools genomecov -bga -ibam PR_merge_134.sort.bam > PR_merge_134.bedGraph
bedtools genomecov -bga -ibam PR_merge_567.sort.bam > PR_merge_567.bedGraph
#bedGraph排序
sort -k1,1 -k2,2n  K27_merge_246.bedGraph -o K27_merge_246.sorted.bedGraph
sort -k1,1 -k2,2n  K27_merge_7810.bedGraph -o K27_merge_7810.sorted.bedGraph
sort -k1,1 -k2,2n  PR_merge_134.bedGraph -o PR_merge_134.sorted.bedGraph
sort -k1,1 -k2,2n  PR_merge_567.bedGraph -o PR_merge_567.sorted.bedGraph
##bedgraph转bw
##因为前面分析是我用uscs的基因组fa文件，为了保持一致，我把fa及fa.fai文件传到/home/data/t170409/data/Aging/hg38_index里了。（你的服务器上用的GCA的）
bedGraphToBigWig K27_merge_246.sorted.bedGraph /home/data/t170409/data/Aging/hg38_index/hg38_ucsc/hg38.fa.fai K27_merge_246.bw
bedGraphToBigWig K27_merge_7810.sorted.bedGraph /home/data/t170409/data/Aging/hg38_index/hg38_ucsc/hg38.fa.fai K27_merge_7810.bw
bedGraphToBigWig PR_merge_134.sorted.bedGraph /home/data/t170409/data/Aging/hg38_index/hg38_ucsc/hg38.fa.fai PR_merge_134.bw
bedGraphToBigWig PR_merge_567.sorted.bedGraph /home/data/t170409/data/Aging/hg38_index/hg38_ucsc/hg38.fa.fai PR_merge_567.bw

3、callpeak

#切换wy环境，你的macs2在环境
conda activate wy
macs2 callpeak -f BAM -t K27_merge_246.sort.bam -n "K27_merge_246" -g hs --nomodel --keep-dup all --outdir  /home/data/t170409/data/wy_cuttag_project/merge
macs2 callpeak -f BAM -t K27_merge_7810.sort.bam -n "K27_merge_7810" -g hs --nomodel --keep-dup all --outdir  /home/data/t170409/data/wy_cuttag_project/merge
macs2 callpeak -f BAM -t PR_merge_134.sort.bam -n "PR_merge_134" -g hs --nomodel --keep-dup all --outdir  /home/data/t170409/data/wy_cuttag_project/merge
macs2 callpeak -f BAM -t PR_merge_567.sort.bam -n "PR_merge_567" -g hs --nomodel --keep-dup all --outdir  /home/data/t170409/data/wy_cuttag_project/merge