制作BW文件的时候需要去除位于黑名单区域的信号

我看到一个biostars论坛提问很有趣

The code I used;

$ computeMatrix scale-regions -S Sample1.bw Sample2.bw Sample3.bw -R genes.bed -a 5000 -b 5000 -o Samples.matrix --regionBodyLength 15000 --skipZeros
$ plotProfile -m Samples.matrix -out Samples.profile.png --perGroup

结果出图很诡异：

How can I remove them?

第一个回答我觉得就是对的：

I expect you have some outlier bin in one gene (just remove that gene, though in the future you'll want to blacklist that region when making bigWig files) that will be apparent in the heatmap.

如果不想在bw文件生成环节修改，也可以

If you want to actually edit the heatmap then don't bother with --outFileNameMatrix, just gunzip the output from computeMatrix, remove the problematic line, change the group_boundaries so they limits are correct, and then gzip the results back up.

当然，这个难度就有点高了，不会脚本很难完成

In general, it's probably simpler to just figure out where the problem region is and remake the bigWig files with that region blacklisted.

Wiggle Track Format (WIG)：http://genome.ucsc.edu/goldenPath/help/wiggle.html

bigWig Track Format ：http://genome.ucsc.edu/goldenPath/help/bigWig.html

BedGraph Track Format ：http://genome.ucsc.edu/goldenPath/help/bedgraph.html

这3种文件格式都是UCSC规定的，所以它提供了系列工具进行互相转换，可以直接下载可执行版本程序：http://hgdownload.cse.ucsc.edu/admin/exe/

常见的工具如下：

• bigWigToBedGraph — this program converts a bigWig file to ASCII bedGraph format.
• bigWigToWig — this program converts a bigWig file to wig format.
• bigWigSummary — this program extracts summary information from a bigWig file.
• bigWigAverageOverBed — this program computes the average score of a bigWig over each bed, which may have introns.
• bigWigInfo — this program prints out information about a bigWig file.