mapcomp

bioinformatics, genetics    

mapcomp通过比较SNP序列在参考近缘种基因组的位置,判断两个图谱中标记的对应关系。

Citation:

Sutherland B J G, Gosselin T, Normandeau E, et al. Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps[J]. bioRxiv, 2016: 039164.

下载安装

在 Github 上: HERE

mapcomp是一系列shell和py脚本,直接下载可用,但是需要依赖以下软件的安装:

  • Linux or MacOS

  • Python 2.7

  • numpy (Python library)

  • bwa

  • samtools

  • The R statistical language

基本用法

注意: 所有指令需要在mapcomp 的根目录下运行, 即"mapcomp"可执行文件所在目录下.

(因为有些shell脚本默认的识别路径是当前目录的某些文件夹)

  1. 将参考基因组复制到mapcomp安装目录中"./02_data/genome/"目录下并重命名为"genome.fasta",建立bwa索引。

     cp XXX.fasta 02_data/genome/genome.fasta
 bwa index 02_data/genome/genome.fasta

  2. 准备SNP标记和连锁群的数据,格式为6列csv格式表格,如下:

    SpeciesName,LG,Position,Zeroes,markerName,markerSequence

    注意:

    • There is no header line in the .csv file

    • There are 6 columns of information

    • The different columns are separated by a comma (,)

    • The fourth column is filled with zeroes (0)

    • You need more than one map in the .csv file

    • You should avoid special characters, including underscores (_) in the marker names.

    ("./01scripts/utilityscripts/findminmaxtotalpositions.py"这个脚本好像是根据""分割数据,所以尽量不要出现"")

    • You must use the period (.) as the decimal separator (no comma (,))

    一个范例csv如下:

    hsapiens,1,0.58,0,marker0001,CGGCACCTCCACTGCGGCACGAAGAGTTAGGCCCCGTGCTTTGCGG

    hsapiens,1,5.74,0,marker0002,CGGCACCTCCACTGCGGCACGAAGAGTTAGGCCCCGTGCTTTGCGG ... hsapiens,1,122.39,0,marker0227,CGGCACCTCCACTGCGGCACGAAGAGTTAGGCCCCGTGCTTTGCGG

  3. 用".csv"文件生成"marker.fasta"

     ./01_scripts/00_prepare_input_fasta_file_from_csv.sh <your_file.csv>

  1. 运行 MapComp

     ./mapcomp

    "mapcomp中可以更改"./01scripts/04pairmarkers.py"的参数"maxdist"(默认为10000000), 参数意义是什么?

    个人认为是认为两个标记配对的最大碱基距离,默认的1E7已经很大了,越小,配对的标记数越少.考虑到参考基因组的scfd长度,这个参数改动一个数量级基本没有影响,可以不纠结它(个人意见)

  2. 查看结果

  • "03mapped/wantedloci.info": the details needed in marker pairs between species.

(can be useful to obtain exact locations of marker mapping on the reference genome)

  • "04_figures": plots comparing between linkage maps

  • "05_results": a summary of results

示例结果如下: