bismark过程中的一个小细节

在最后一步bismark_methylation_extractor的时候，输出的.bedGraph 和 .bismark.cov是空文件，在目标目录下有一大堆的.temp文件。看了mapping这一步的结果的report和summary，是没有问题的。那肯定是哪里有问题了。

各种检索，终于是发现了问题所在，参考no bedGraph output #180:

Your genome of interest seems to contain tens of thousands of scaffolds which makes it difficult to write to temporary files as we can do for chromosome based genomes. I recommend you use the option --scaffolds to fix this. This is taken from the bismark2bedGraph help file:

于是，我把这个参数加上了，然后就正常了。

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推荐一个不错的甲基化分析教程：

DNA-Methylation-Sequencing-Analysis-with-WGBS