Macs2做差异peak分析
参考:https://github.com/macs3-project/MACS/wiki/Call-differential-binding-events
差异peak分析的软件很多,但是针对无生物学重复的单一样本来说,只能用MACS2的bdgdiff来实现。
1、预测插入片段长度(这一步还没理解)
这一步在call peak的时候会显示。即使没有记录,也可以通过predictd命令来查看
macs2 predictd -i Input_0h.rmdup.bam
#SRR13579713 total tags in treatment: 23713766
predicted fragment length is 291 bps
#SRR13579715 total tags in treatment: 23914681
predicted fragment length is 294 bps
#SRR13579716 total tags in treatment: 21077141
#SRR13811453 total tags in treatment: 27928295
predicted fragment length is 137 bps
#SRR13811454 total tags in treatment: 23931262
#H3K4_input_0h total tags in treatment:8847498
#H3K4_input_4h total tags in treatment:21180079
2、call peak
做这一步的时候加上-B 让同时输出bedgradh格式。
macs2 callpeak -B -n "H3K27ac_hCG_4h" --keep-dup all -t SRR13579715.rmdup.bed -c SRR13579716.rmdup.bed -g mm --board-cutoff 0.1
3、差异分析
macs2 bdgdiff --t1 H3K27ac_hCG_0h_treat_pileup.bdg --c1 H3K27ac_hCG_0h_control_lambda.bdg --t2 H3K27ac_hCG_4h_treat_pileup.bdg --c2 H3K27ac_hCG_4h_control_lambda.bdg --d1 21077141 --d2 21077141 -g 60 -l 147 --o-prefix ac_0h_vs_4h
OK!!