预测adapter--minion
如果我们不知道数据的接头，该怎么办呢？
minion 由 The European Bioinformatics Institute（EBI）开发，可用于预测接头。
一、安装
安装minion，参见EBI-Kraken网站
linux下载网址:
http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/binaries/reaper-13-100/linux/
二、用法
使用方法非常简单：
minion search-adapter -i SRR.fastq
预测adapter的结果示例：
criterion=sequence-density
sequence-density=52.19
sequence-density-rank=1
fanout-score=31.57
fanout-score-rank=1
prefix-density=54.75
prefix-fanout=30.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACACACATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA
criterion=fanout-score
sequence-density=52.19
sequence-density-rank=1
fanout-score=31.57
fanout-score-rank=1
prefix-density=54.75
prefix-fanout=30.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACACACATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA
大多数情况下，选取第一个预测结果（criterion=sequence-density）为adapter。为什么呢？
The two criteria are unfortunately necessary due to the varying charachteristics of 3' adapter sequence in different experimental protocols. The first criterion is frequency of occurrence; the second criterion incorporates a fan-out measure that captures the typical characteristic of 3' adapter sequence of being attached to a multitude of different prefixes. When infering adapters (i.e. without using-adapter) two candidate sequences will be shown. The second will start with the linecriterion=fanout-score. The second should only be considered if the first candidate is clearly a biological sequence. This can be established by using one of theBLASTinterfaces provided for example byNCBIandENSEMBL. 也就是说，只有在第一个序列确认为是有生物学意义时，才考虑第二个序列（criterion=fanout-score）。可以用NCBI或ENSEMBL的BLAST平台来确认是否有生物学意义
三、讨论
minion寻找到的接头一定要用Google或者Baidu搜索，确认是否存在该接头。
因为minion的结果不一定就是接头，只是用来预测。
接下来也是使用cutadapt或其他软件去掉接头。参考前文即可。
参考资料
