2.7.1 mummer共线性分析

mummer
link

代码参考
（输出文件为默认的out.delta）

#MummerSNP：
nucmer --maxmatch -c 90 -l 40 RF-2022.fna DSM13.fna &&
delta-filter -r -q out.delta > out-filter.delta &&
show-snps out-filter.delta > SNP_Indel.txt

#MummerSynteny：
mummer –mum –b –c –l 30 ref.fasta query.fasta > out.mummer &&
mummerplot –postscript out.mummer &&
out.ps 
#(convert to pdf)

plot报错：

gnu-plot

检索答案：
mummerplot is compatible with gnuplot v4. Some things changed in v5. You can either revert to v4, or edit the mummerplot script to comment out the line that produces this "set mouse" option that it complains about.

方法一：通过conda安装gnu-plot 4.6
重新运行报错。放弃。

Can't find PostScript prologue file prologue.ps
loadpath is empty
gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
no XAPPLRESDIR found in the environment,
falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories or set the environmental variable GNUPLOT_PS_DIR or set the loadpath appropriately

方法二：gnuplot V5 ，将mummerplot脚本中set mouse的三行命令注释掉
set mouse mouseformat "[%.0f, %.0f]"在一起的三行

问题：通过mummer比对来调整参考基因组和query基因组的起点和正反，保持一致。1）如果方向相反，先调整方向 2）然后切割再拼接

lastz

输出maf文件
整理参照link

lastz输出的maf文件格式
行1 a
行2 s ref
行3 s query
行4 空行
...
屏幕快照 2017-11-11 上午9.37.37.png
每一行各列的意义：
s NC_002947.4 0 4538 + 6181873 AACTGC
1:genome_id 2:起始位点 3:终止位点 4:链正反 5：fasta总长 6:序列