linux command line skill (display and sort the file based on their size)

ll -S -h| grep ‘^[^d]’   -rw-r–r– 1 shenzy shenzy 3.3M 2012-01-18 10:13 Patrick_Lee_lastVersion.rar -rw-r–r– 1 shenzy shenzy 3.2M 2012-01-18 17:50 Patrick_Lee_update.rar -rw-r–r– 1 shenzy shenzy 899K 2011-11-25 18:10 metagenomic_phylogenetic_tree.ppt -rw-r–r– 1 shenzy shenzy 44[……]

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R abundance curve

install.packages("BiodiversityR")
library(BiodiversityR)
library(vegan) data(dune.env) data(dune) RankAbun.1 <- rankabundance(dune) RankAbun.1 rankabunplot(RankAbun.1,scale='abundance', addit=FALSE, specnames=c(1,2,3)) rankabuncomp(dune, y=dune.env, factor='Management', scale='propo[......]

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awk 一些简单的用法

# 打印每行,并删除第二列

  • awk ‘{ $2 = “”; print }’ file1
  • awk ‘{ $2 = “”;$1 = “”; print }’ test1
# 打印部分文本
bash-3.2$ # 打印文件的前十行 (模拟 “head”)   bash-3.2$ awk ‘NR < 11′ test1     # 打印文件的最后两行 (模拟 “tail -2″awk ‘{y=x “\n” $0; x=$0};END{print y}’   # 打印文件的最后[……]

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Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes.

 

Description

 

Cake is a bioinformatics tool to identify putative somatic mutations from cancer genome/exome data. Cake combines somatic calls from a number of publicly available SNP/somatic variant calling tools with an array of variant filtering modules to discard unwanted

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Mothur 命令手册-Mothur命令中文解释

Align.check 这个命令使你计算16S rRNA基因序列中潜在的错配碱基对数目。如果你对ARB(http://www.arb-home.de/)的编辑窗口熟悉的话,这与计算~,#,-和=这些符号的数目相同。用greengenes的二级结构图谱和esophagus dataset运行这个命令。要运行这个命令,你必须提供FASTA格式的序列文件。 Align.seqs 这个命令把用户提供的FASTA格式的候选序列文件对齐到用户提供的同样格式的模板序列。通用的方法是: 1.采用kmer searching(http://sourceforge.net/apps/mediawiki/k[……]

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