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

一到一还谈什么随机？

如果是一个文件夹中的文件随机复制到N个文件夹中的一个，那么可以把N个文件夹的路径放到一个数组变量中，并用 $RANDOM 来产生随机数，对数组长度取余后作为下标。

#!/bin/bash

dests=( /dest/a /dest/b /dest/c /destd)

for f in * do

    cp "$f" ${dests[((RANDOM%${#dests[@]}))]

done

#！/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.

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