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MHanalyser使用说明

2018/3/30 11:15:47      点击:

MHanalyser

Zheng Li, Peng Chen and Feng Chen

Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P.R. China.

    After FLfinder analysis, we can get the alleles and corresponding read depth of microhaplotype loci from ‘FASTQ’ file. However, the results generated by FLfinder contain numerous repeated alleles due to the sequencing mistake, which add difficulty for data processing, particularly when handling large number of samples. The program MHanalyser has been developed to classify the results into a more readable form by three steps.

First step: Input files

The input file consists of four columns in an excel form. (1) Individual: marking different samples by using numbers or letters. (2) Reads: the number of sequencing reads. (3) Loci: the names of microhaplotype loci. (4) SNP: alleles of each microhap locus, which contain several SNPs as a haplotype (e.g. ‘TTT’). Tips: The names of four parts cannot be changed. We also provided an example file named “test.xlsx”.

Second step: Analysis

Start the program and pull the input file into the program. After pushing “Enter”, the program will prompt you the finish information. And you will get a “result.csv” file.

Last step: Results

In the result file, the first column indicates the names of all the microhap loci and their corresponding alleles, while the first row demonstrates the samples’ No.. The rest information in the cross table are sequencing depth of each allele.

 

MHanalyser使用说明

李峥 陈鹏 陈峰

南京医科大学法医学系江苏 南京211166

FLfinder软件可以用于FASTQ文件的分析,并获得微单倍型位点的分型结果,但是该软件得到的结果整理起来较为困难,尤其是处理多个样本多个位点时,常常由于测序错误等原因,出现多个重复的等位基因,为数据处理增加了难度。

本程序对Flfinder得到的结果进行整理,以得到更易阅读的数据格式,并能将多个样本的数据汇总在一起,具体步骤如下。

1.输入文件:

输入文件格式为excel,由四列组成:(1)Individual, 为不同个体的编号,数字或字母均可;(2)Reads,为每个等位基因的测序深度,即测得序列的重复次数;(3)Loci,为每个微单倍型位点的名称;(4)SNP,为每个微单倍型位点的等位基因,即多个SNP组成的单倍型序列。注:表头的命名Individual, Reads, LociSNP名称和顺序固定,不可替换。我们提供了一个输入文件的示例“test.xlsx”

2.分析:

运行程序MHanalyser,待弹出对话窗口后,按照提示将将整理好的excel表格拖入对话框中,待提示分析完成后,可以得到一个结果文件result.csv。

3.得到结果:

在得到的结果文件中,第一列为位点以及等位基因的名称,第二列开始,第一行为不同个体的样本编号,其余行为对应等位基因的测序深度。