生信理论及操作

bsub -q interactive -Is bash
for i in *.lsf;do bsub < ${i};done
muscle3.8.31_i86linux64 -in fa -out afa -clw
module load seqkit/0.11.0
取反向互补序列
seqkit seq test.fa -r -p > test_re_com.fa
seqkit seq b73.fa -w 0 > b73_out.fa

RNA-seq
【系列】转录组入门（1）：软件准备 https://www.plob.org/article/11457.html

SRA下载
SRA 数据下载自救指南 https://www.jianshu.com/p/19ae29e54c59
NGS小技能（2）：如何进行SRA到fastq格式的快速转换 https://www.jianshu.com/p/4779b7103ae1
SRA Run Selector https://www.ncbi.nlm.nih.gov/Traces/study/?
GEO http://www.ncbi.nlm.nih.gov/geo/
都8102年了，还用fastq-dump，快换fasterq-dump吧 https://www.jianshu.com/p/5c97a34cc1ad

blast
这或许是我写的最全的BLAST教程 https://www.jianshu.com/p/de28be1a3bea
【数据库】本地NR数据库如何按物种拆分？ https://www.cnblogs.com/jessepeng/p/13736609.html
如何利用NR库快速进行物种鉴定 https://www.jianshu.com/p/45fdb5cf930a

       qaccver - Query accesion.version
       saccver - Subject accession.version
        pident - Percentage of identical matches
        length - Alignment length
      mismatch - Number of mismatches
       gapopen - Number of gap openings   
        qstart - Start of alignment in query
          qend - End of alignment in query
        sstart - Start of alignment in subject
          send - End of alignment in subject
        evalue - Expect value
      bitscore - Bit score

[-db database_name]
[-taxids taxids]
[-query input_file]
[-out output_file]
[-evalue evalue]
[-outfmt format]
[-max_target_seqs num_sequences]
[-num_threads int_value]
 -html
 -sorthits <Integer, (>=0 and =<4)>

植物转录因子数据库
PlantRegMap http://plantregmap.gao-lab.org/
PlantTFDB http://planttfdb.gao-lab.org/

时序RNA-seq分析
时序RNA-Seq差异表达分析软件比较 https://www.jianshu.com/p/7ec4fa1c6838
Mfuzz

ChIP-seq
第3篇：用MACS2软件call peaks https://www.jianshu.com/p/21e8c51fca23
利用bedtools预测chip_seq数据的靶基因 https://blog.csdn.net/weixin_43569478/article/details/108079464
ChIP-seq产生的文件解读 https://blog.csdn.net/sunyu_03/article/details/82633799

基本数据处理
shell 第一列相同则拼接第二列 https://blog.csdn.net/weixin_33700350/article/details/92654968
EXCEL判断第一列如果相同，则合并第二列中的值到一个单元格，中间用逗号隔开 https://zhidao.baidu.com/question/1860633839081791987.html
shell除法计算 https://blog.51cto.com/5iwww/270119
shell-awk 按列求和总结 https://blog.csdn.net/weixin_34262482/article/details/92605125
shell脚本-批量替换文件中的多组字符串 https://blog.csdn.net/luo617/article/details/84880168

PCA
一文看懂主成分分析 https://cloud.tencent.com/developer/article/1167713
PCA-弱水三千，取哪一瓢饮？ https://www.jianshu.com/p/f20bd286ce32
Plotting PCA (Principal Component Analysis) https://cran.r-project.org/web/packages/ggfortify/vignettes/plot_pca.html

IGV
测序数据可视化（二）- IGV https://cloud.tencent.com/developer/article/1036706

bedtools igv -i input.bed

保存igv的信息，igvtools接口的使用：将igvtools查看bam文件的结果保存为txt文件，并提取信息 https://blog.csdn.net/a_giant_pig/article/details/103011731
bam文件的可视化（测序深度） | IGV https://www.jianshu.com/p/c0635eb9ac24
基因组浏览器IGV实践 https://www.jianshu.com/p/4089d07ba239
学IGV必看的初级教程 https://cloud.tencent.com/developer/article/1050826
Running IGV with a batch file https://software.broadinstitute.org/software/igv/batch
File Formats https://software.broadinstitute.org/software/igv/IGV

如何快速找到某个基因的结构域和保守位点 https://www.sohu.com/a/216315762_419916
snapgene入门视频 https://www.snapgene.com/support/tutorial-videos/?referrer=SnapGene

RPKM vs FPKM vs TPM http://www.genek.tv/article/23
TPM、read counts、RPKM/FPKM你选对了吗？ http://blog.sciencenet.cn/blog-3372875-1089851.html

表达矩阵的归一化和标准化，去除极端值，异常值 https://mp.weixin.qq.com/s/KQgWCdZ42EcqV_Qzc2wmTw
Z-Score数据标准化 https://www.cnblogs.com/itboys/p/10861492.html

STDEV是样本标准差的函数，STDEVP是总体标准差的函数。
如是总体（即估算总体方差），根号内除以n（对应excel函数：STDEVP）；
如是抽样（即估算样本方差），根号内除以（n-1）（对应excel函数：STDEV）；
因为我们大量接触的是样本，所以普遍使用根号内除以（n-1）。

Question: Error while doing indexing of fasta file using SAMTOOL faidx https://www.biostars.org/p/229449/

GWAS
GWAS | 原理和流程 | 全基因组关联分析 | Linkage disequilibrium (LD)连锁不平衡 | 曼哈顿图 Manhattan_plot | QQ plot https://www.cnblogs.com/leezx/p/9013615.html
动植物GWAS群体知多少 https://www.sohu.com/a/207046986_761120
全基因组关联分析 (GWAS) - 简介 https://www.jianshu.com/p/acdc4a22e30a
扒一扒遗传分析中群体那些事儿 http://blog.sciencenet.cn/home.php?mod=space&uid=1094241&do=blog&id=1093008