CUT&Tag數(shù)據(jù)隨筆記錄

1.要做一個(gè)H3K27ac與PR的互作分析熱圖。

1.1樣本的合并以及取交集peak
分別對(duì)每一個(gè)樣本callpeak得到5w左右peak。如果將3個(gè)樣本合并，再callpeak則得到36w個(gè)peak，不知什么原因?qū)е?。還是準(zhǔn)備取三個(gè)樣本的common peaks，放棄合并三個(gè)樣本bam文件再callpeak的實(shí)驗(yàn)方法。

1.2如何取三個(gè)生物學(xué)重復(fù)樣本的common peak
參考文章：http://www.itdecent.cn/p/d8a7056b4294
方法（1）：利用bedtools工具

bedtools intersect \
-a PR-3_peaks.narrowPeak \
-b PR-4_peaks.narrowPeak PR-6_peaks.narrowPeak \
>/home/data/t170409/data/wy_cuttag_project/callpeak/common_peaks/PR_young_overlaps.bed

再以輸出的common peak 的bed文件進(jìn)行后續(xù)分析

image.png

一些常見參數(shù)如下

-wo：Write the original A and B entries plus the number of base pairs of overlap between the two features.
-wa：Write the original entry in A for each overlap.
-v：Only report those entries in A that have no overlaps with B

如果只有-a和-b參數(shù)，返回的是相對(duì)于A的overlaps。加上參數(shù)-wo返回A和B原始的記錄加上overlap的記錄。參數(shù)-wa返回每個(gè)overlap中A的原始記錄。

image.png