生信小tips

TBtools富集过程中的一些小 *** 作

fasta2phy:

cat 4.4Dsites.pl.connect4Dsites.fa | tr '\n' '\t' | \

pipe pipe>sed 's/>/\n/g' |

pipe pipe pipe>sed 's/\t//' | sed 's/\t//g' |

pipe pipe pipe pipe pipe>awk 'NF >0' >4.4Dsites.pl.connect4Dsites.fa.tmp

awk '{print " "NR" "length($2)}' 4.4Dsites.pl.connect4Dsites.fa.tmp |

pipe>tail -n 1 | \

pipe pipe>cat - 4.4Dsites.pl.connect4Dsites.fa.tmp >4.4Dsites.pl.connect4Dsites.phy

fasteprr 分型报错！

zcat input.vcf.gz | perl -pe "s/\s.:/\t./.:/g" | bgzip -c >output.vcf.gz

Structure

For population structure

analyses, we discarded SNPs with missing rate >20%

and minor allele frequency (MAF) <5%. We also excluded

highly correlated SNPs by performing an LD-based SNP

pruning process in PLINK v1.90

Mental test

VEGAN(R package)

质控软件

trimmomatic (需要知道接头序列)

FSC

We excluded SNPs from three genomic regions

under long-term balancing selection (see the “Balancing

selection in B. stricta genomes” section) and only used

fourfold degenerate sites and intergenic regions, because

they are less affected by selection.

To account for the influence of effective population

size on estimated ρ, we divided ρ by diversity (π) in

each 20-kb window following Wang et al. [4] and compared

ρ/π between islands and the rest of the genome.

提取奇数行 sed -n '1~2p' a.txt

提取偶数行 sed -n '0~2p' a.txt

Linux文件随机抽取N行：

shuf -n100 filename

sort -R filename | head -n100

awk '{x+=1}{print 3"\t"$4}' test.map >map

其中 ： tree 文件夹中： estimated_gene_trees.tree 基因树

estimated_species_tree.tree 并联树

name 文件：

singularity sif 转 sandbox

几款构建祖先染色体的软件

#！/bin/bash

sort -R a.txt | head -20000

##

sort随机排序，然后取前20000，实现出来就是随机抽取20000.

一、从第3000行开始，显示1000行。即显示3000~3999行

cat filename | tail -n +3000 | head -n 1000

二、显示1000行到3000行

cat filename| head -n 3000 | tail -n +1000

注意两种方法的顺序

分解：

tail -n 1000：显示最后1000行

tail -n +1000：从1000行开始显示，显示1000行以后的

head -n 1000：显示前面1000行

三、用sed命令

sed -n '5,10p' filename 这样就可以只查看文件的第5行到第10行。

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