bedgraph file(For ChIP-Seq) 怎么做 Z-Score transformation? - 未名空间MITBBS历史存档

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bedgraph file(For ChIP-Seq) 怎么做 Z-Score transformation?

bedgraph file(For ChIP-Seq) 怎么做 Z-Score transformation?# Biology - 生物学

m*52016-12-28 08:12

1 楼

如题，看到有的文章上chip Seq signal是用Z-Score transformed的
看起来很sharp很好看，另外也能强调组之间pattern 变化而不是绝对信号强弱。
有没什么现成package可以做到的，还是要自己code
谢谢大牛指点啦！

r*z2016-12-28 08:12

2 楼

我觉得是一开始在peak calling 的时候就把 z-score 算出来了。
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM896741
The sequencing data from matching input samples are used for the processing
of ChIP data, as a measure of background signal which might be significant.
After normalizing the input data to match the number of tags in the ChIP
data, the number of input tags is subtracted from the number of ChIP tags in
the target window before calculating its z-score. In addition, ChIP
hotspots were refined into 150 bp peaks using a peak-finding procedure. For
each hotspot, a new z-score ‘peak z’ was computed similarly as for hotspot
detection, but instead using a 150 bp window within the hotspot and the
hotspot as the target window and local background window, respectively. The
peak z score was computed scanning through the hotspot with bp resolution
for all possible 150 bp windows. A putative peak is defined as a 150 bp
window whose peak z score is above 30.

j*g2016-12-28 08:12

3 楼

请问这个z-score转换后，再看tracks，是吗？

processing
.
in
For
hotspot

【在 r***z 的大作中提到】

: 我觉得是一开始在peak calling 的时候就把 z-score 算出来了。
: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM896741
: The sequencing data from matching input samples are used for the processing
: of ChIP data, as a measure of background signal which might be significant.
: After normalizing the input data to match the number of tags in the ChIP
: data, the number of input tags is subtracted from the number of ChIP tags in
: the target window before calculating its z-score. In addition, ChIP
: hotspots were refined into 150 bp peaks using a peak-finding procedure. For
: each hotspot, a new z-score ‘peak z’ was computed similarly as for hotspot
: detection, but instead using a 150 bp window within the hotspot and the