生信人的Linux20题

生信人的linux考试.png

1、创建文件夹：

vip41@VM-0-15-ubuntu:~/linux练习题$ mkdir -p 1/2/3/4/5/6/7/8/9
vip41@VM-0-15-ubuntu:~/linux练习题$ cd 1
vip41@VM-0-15-ubuntu:~/linux练习题/1$ tree 
.
└── 2
    └── 3
        └── 4
            └── 5
                └── 6
                    └── 7
                        └── 8
                            └── 9

2、3、创建.txt文件并往文件内写东西 ：两种方法：
第一种方法：

vip41@VM-0-15-ubuntu:~/linux练习题/1$ cd 2/3/4/5/6/7/8/9/
vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ touch me.txt
vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ ls -lh
total 0
-rw-rw-r-- 1 vip41 vip41 0 Dec 16 22:58 me.txt
vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ cat >me.txt
Go to: http://www.biotrainee.com/
I love bioinfomatics.
And you ?
^C
vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ cat me.txt 
Go to: http://www.biotrainee.com/
I love bioinfomatics.
And you ?

第二种办法：

vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ cat >me.txt
Go to: http://www.biotrainee.com/
I love bioinfomatics.
And you ?
^C
vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ cat me.txt 
Go to: http://www.biotrainee.com/
I love bioinfomatics.
And you ?
vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ ls -lh
total 4.0K
-rw-rw-r-- 1 vip41 vip41 66 Dec 16 23:03 me.txt

4、删除所有创建的文件夹及文件：

vip41@VM-0-15-ubuntu:~/linux练习题/1/2/3/4/5/6/7/8/9$ cd ~/linux练习题/
vip41@VM-0-15-ubuntu:~/linux练习题$ rm -r 1
vip41@VM-0-15-ubuntu:~/linux练习题$ ls -lh
total 4.9M
-rw-rw-r-- 1 vip41 vip41 2.6M Jan 11  2017 hg38.tss
drwxrwxr-x 4 vip41 vip41 4.0K Nov 12  2016 rmDuplicate
-rw-rw-r-- 1 vip41 vip41 103K Nov 12  2016 rmDuplicate.zip
drwxrwxr-x 3 vip41 vip41 4.0K Dec 14 23:32 sickle-results
-rw-rw-r-- 1 vip41 vip41 2.3M Oct  6  2016 sickle-results.zip
-rw-rw-r-- 1 vip41 vip41 3.1K May 18  2017 test.bed
#文件夹1已被删除

5、创建 folder1~5这5个文件夹，然后每个文件夹下面继续创建 folder1~5这5个文件夹：mkdir -p folder_{1..5}/folder_{1..5}


image.png

6、在第五题创建的每一个文件夹下面都 创建第二题文本文件 me.txt ，内容也要一样：
xargs 一般是和管道一起使用
somecommand |xargs -item command


image.png

7、删除之前的文件夹及文件：


image.png

8、下载 http://www.biotrainee.com/jmzeng/igv/test.bed 文件，后在里面选择含有 H3K4me3 的那一行是第几行，该文件总共有几行。

image.png
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9、下载 http://www.biotrainee.com/jmzeng/rmDuplicate.zip 文件，并且解压，查看里面的文件夹结构

vip41@VM-0-15-ubuntu:~/biosoft/data1$ wget  http://www.biotrainee.com/jmzeng/rmDuplicate.zip
--2018-12-13 22:09:18--  http://www.biotrainee.com/jmzeng/rmDuplicate.zip
Resolving www.biotrainee.com (www.biotrainee.com)... 123.206.72.184
Connecting to www.biotrainee.com (www.biotrainee.com)|123.206.72.184|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 104931 (102K) [application/zip]
Saving to: ‘rmDuplicate.zip’

rmDuplicate.zip   100%[===========>] 102.47K   551KB/s    in 0.2s    

2018-12-13 22:09:19 (551 KB/s) - ‘rmDuplicate.zip’ saved [104931/104931]
# 解压文件
vip41@VM-0-15-ubuntu:~/biosoft/data1$ unzip rmDuplicate.zip 
Archive:  rmDuplicate.zip
   creating: rmDuplicate/
   creating: rmDuplicate/picard/
   creating: rmDuplicate/picard/paired/
  inflating: rmDuplicate/picard/paired/readme.txt  
  inflating: rmDuplicate/picard/paired/tmp.header  
  inflating: rmDuplicate/picard/paired/tmp.MarkDuplicates.log  
  inflating: rmDuplicate/picard/paired/tmp.metrics  
  inflating: rmDuplicate/picard/paired/tmp.rmdup.bai  
  inflating: rmDuplicate/picard/paired/tmp.rmdup.bam  
  inflating: rmDuplicate/picard/paired/tmp.sam  
  inflating: rmDuplicate/picard/paired/tmp.sorted.bam  
   creating: rmDuplicate/picard/single/
  inflating: rmDuplicate/picard/single/.MarkDuplicates.log  
  inflating: rmDuplicate/picard/single/readme.txt  
  inflating: rmDuplicate/picard/single/tmp.header  
  inflating: rmDuplicate/picard/single/tmp.MarkDuplicates.log  
  inflating: rmDuplicate/picard/single/tmp.metrics  
  inflating: rmDuplicate/picard/single/tmp.rmdup.bai  
  inflating: rmDuplicate/picard/single/tmp.rmdup.bam  
  inflating: rmDuplicate/picard/single/tmp.sam  
  inflating: rmDuplicate/picard/single/tmp.sorted.bam  
   creating: rmDuplicate/samtools/
   creating: rmDuplicate/samtools/paired/
  inflating: rmDuplicate/samtools/paired/readme.txt  
  inflating: rmDuplicate/samtools/paired/tmp.header  
  inflating: rmDuplicate/samtools/paired/tmp.rmdup.bam  
  inflating: rmDuplicate/samtools/paired/tmp.rmdup.vcf.gz  
  inflating: rmDuplicate/samtools/paired/tmp.sam  
  inflating: rmDuplicate/samtools/paired/tmp.sorted.bam  
  inflating: rmDuplicate/samtools/paired/tmp.sorted.vcf.gz  
   creating: rmDuplicate/samtools/single/
  inflating: rmDuplicate/samtools/single/readme.txt  
  inflating: rmDuplicate/samtools/single/tmp.header  
  inflating: rmDuplicate/samtools/single/tmp.rmdup.bam  
  inflating: rmDuplicate/samtools/single/tmp.rmdup.vcf.gz  
  inflating: rmDuplicate/samtools/single/tmp.sam  
  inflating: rmDuplicate/samtools/single/tmp.sorted.bam  
  inflating: rmDuplicate/samtools/single/tmp.sorted.vcf.gz
# 查看文件夹结构     
vip41@VM-0-15-ubuntu:~/biosoft/data1/rmDuplicate$ tree
.
├── picard
│   ├── paired
│   │   ├── readme.txt
│   │   ├── tmp.header
│   │   ├── tmp.MarkDuplicates.log
│   │   ├── tmp.metrics
│   │   ├── tmp.rmdup.bai
│   │   ├── tmp.rmdup.bam
│   │   ├── tmp.sam
│   │   └── tmp.sorted.bam
│   └── single
│       ├── readme.txt
│       ├── tmp.header
│       ├── tmp.MarkDuplicates.log
│       ├── tmp.metrics
│       ├── tmp.rmdup.bai
│       ├── tmp.rmdup.bam
│       ├── tmp.sam
│       └── tmp.sorted.bam
└── samtools
    ├── paired
    │   ├── readme.txt
    │   ├── tmp.header
    │   ├── tmp.rmdup.bam
    │   ├── tmp.rmdup.vcf.gz
    │   ├── tmp.sam
    │   ├── tmp.sorted.bam
    │   └── tmp.sorted.vcf.gz
    └── single
        ├── readme.txt
        ├── tmp.header
        ├── tmp.rmdup.bam
        ├── tmp.rmdup.vcf.gz
        ├── tmp.sam
        ├── tmp.sorted.bam
        └── tmp.sorted.vcf.gz

10、打开第九题解压的文件，进入 rmDuplicate/samtools/single 文件夹里面，查看后缀为 .sam 的文件，搞清楚 生物信息学里面的SAM/BAM 定义是什么。


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  • SAM(Sequence Alignment/Map)格式是一种通用的比对格式，用来存储reads到参考序列的比对信息。
    SAM是一种序列比对格式标准，由sanger制定，是以TAB为分割符的文本格式。主要应用于测序序列mapping到基因组上的结果表示，当然也可以表示任意的多重比对结果。SAM分为两部分，注释信息（header section）和比对结果部分（alignment section）。
  • BAM是SAM的二进制格式，因此两者格式相同，只是BAM文件占用储存空间更小，运算更快。
    具体参考：https://www.jianshu.com/p/9c99e09630da

11、安装 samtools 软件：
第一种办法;
1、先安装miniconda: 用wget 下载miniconda, bash .sh文件，进行安装，一直回车，直到提示回复y/n，选择y, 直到安装成功。source ~/.bashrc 激活conda, 验证可用。

image.png

2、先查找是否有Samtools可安装
image.png

缺乏频道，无法安装，需要更改镜像源。
加入一些与生物相关的镜像源：
2018-11-24_203035.png

3、用conda下载samtools:
image.png

samtools可用：
image.png

第二种办法：
用wget下载samtools，步骤如下 :

echo 'export PATH=/home/vip41/biosoft/samtools/bin:$PATH' >>~/.bashrc 
source ~/.bashrc
cd ~/biosoft/ samtools 
 wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -xvfz samtools-1.9.tar.bz2
cd  samtools-1.9
./configure --prefix=/home/vip41/biosoft/samtools  
make && make install

附：linux下 的软件安装需要指定路径，而且是自己有权限的路径。
验证samtools可用：

Program: samtools (Tools for alignments in the SAM format)
Version: 1.9 (using htslib 1.9)

Usage:   samtools <command> [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     fqidx          index/extract FASTQ
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags
     markdup        mark duplicates

  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA

  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)

  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM

samtools可用，但是基本命令如ls、pwd等无法使用，使用该命令（export PATH=/bin:/usr/bin:/usr/local/bin:/sbin:/usr/sbin
）解决ls等基本命令无法使用问题，但是samtools又变成无法使用，重新添加环境变量，samtools可用，但是ls等基本命令又无法使用：

vip41@VM-0-15-ubuntu:~/biosoft/samtools$ echo 'export PATH=/home/vip41/biosoft/samtools/bin:$PATH'>>~/.bashrc
vip41@VM-0-15-ubuntu:~/biosoft/samtools$ source ~/.bashrc
vip41@VM-0-15-ubuntu:~/biosoft/samtools$ ls
Command 'ls' is available in '/bin/ls'
The command could not be located because '/bin' is not included in the PATH environment variable.
ls: command not found
vip41@VM-0-15-ubuntu:~/biosoft/samtools$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.9 (using htslib 1.9)

Usage:   samtools <command> [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     fqidx          index/extract FASTQ
     index          index alignment

解决办法，使用命令vi ~/.bashrc删除samtools的路径，问题解决。详见：https://www.jianshu.com/p/57abd0804df6

12、打开 后缀为BAM 的文件，找到产生该文件的命令。

  1. 使用find命令先找到.bam的文件:
vip41@VM-0-15-ubuntu:~$ find ~ -name  '*.bam'
/home/vip41/biosoft/htslib/htslib-1.9/test/range.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/bedcov/bedcov.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/quickcheck/1.quickcheck.badeof.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/quickcheck/3.quickcheck.ok.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/quickcheck/2.quickcheck.badheader.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/quickcheck/4.quickcheck.ok.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/stat/11_target.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/stat/12_overlaps.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/mpileup.1.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/ce#5b.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/ce#unmap1.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/xx#triplet.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/c1#ID.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/mpileup.3.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/mpileup.2.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/c1#clip.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/ce#unmap.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/overlapIllumina.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/ce#unmap2.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/ce#large_seq.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/c1#pad1.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/c1#pad3.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/xx#minimal.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/c1#pad2.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/c1#ID2.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/mpileup-E.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/mpileup/1read.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/dat/test_input_1_a.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/dat/test_input_1_c.bam
/home/vip41/biosoft/samtools/samtools-1.9/test/dat/test_input_1_b.bam
/home/vip41/biosoft/samtools/samtools-1.9/htslib-1.9/test/range.bam
/home/vip41/linux练习题/rmDuplicate/picard/paired/tmp.rmdup.bam
/home/vip41/linux练习题/rmDuplicate/picard/paired/tmp.sorted.bam
/home/vip41/linux练习题/rmDuplicate/picard/single/tmp.rmdup.bam
/home/vip41/linux练习题/rmDuplicate/picard/single/tmp.sorted.bam
/home/vip41/linux练习题/rmDuplicate/samtools/paired/tmp.rmdup.bam
/home/vip41/linux练习题/rmDuplicate/samtools/paired/tmp.sorted.bam
/home/vip41/linux练习题/rmDuplicate/samtools/single/tmp.rmdup.bam
/home/vip41/linux练习题/rmDuplicate/samtools/single/tmp.sorted.bam

2）使用命令samtools view查看.bam文件：

vip41@VM-0-15-ubuntu:~/linux练习题/rmDuplicate/samtools/paired$ samtools view tmp.rmdup.bam 
D00691:39:C7HGRANXX:7:1102:7445:18770   99  chr10   93614   60   126M   =   93621   133 GGCACGTGGTGACCCCACTCATGGTAGCAGACACCAGGTGGTTCAGGTCACCATAGGTGGGTGTGGGCAGTTTTAGGGTCTTGGAACATATGTCATACAGAGCTTCGTTATCTATGCAAAAGGTCT  BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  NM:i:0  MD:Z:126    AS:i:126    XS:i:111     XA:Z:chr3,-197846908,126M,3;chr9,-141070974,126M,3;chr1,-808987,126M,4;chr4,+190904265,126M,4; MQ:i:60
D00691:39:C7HGRANXX:7:1102:7445:18770   147 chr10   93621   60   126M   =   93614   -133    GGTGACCCCACTCATGGTAGCAGACACCAGGTGGTTCAGGTCACCATAGGTGGGTGTGGGCAGTTTTAGGGTCTTGGAACATATGTCATACAGAGCTTCGTTATCTATGCAAAAGGTCTCATCTGC  FFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFBBBBB  NM:i:0  MD:Z:126    AS:i:126    XS:i:111     XA:Z:chr9,+141070967,126M,3;chr3,+197846902,1S125M,3;  MQ:i:60
D00691:39:C7HGRANXX:7:2302:14294:49245  323 chr10   94741   5    56H70M chr9    140136176   0   CACCGGTGGCTTCGTTGTAGTACACGTTGATGCGCTCCAGCTGGAGGTCGCTATCTCCGTGGTAAGTGCC  FFFFFFFFFFFFFF<FFBFFFFFFFFFBFFFFFFFFFFBFFFFFFFB7FFFBFFFFFFFFFFFFBFFFFF  NM:i:7  MD:Z:5C4C32C4G3G2C8G5   AS:i:35 XS:i:30 SA:Z:chr9,140136365,-,69S57M,53,4;   XA:Z:chrY,+19630445,56S70M,8;chrY,-20549264,70M56S,8;
D00691:39:C7HGRANXX:7:2201:12400:93441  387 chr10   94741   6    67H59M chr9    140136365   0   CACCGGTGGCTTCGTTGTAGTACACGTTGATGCGCTCCAGCTGGAGGTCGCTATCTCCG FFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:6  MD:Z:5C4C32C4G3G2C3 AS:i:33 XS:i:28 SA:Z:chr9,140136365,-,58S68M,46,6;  XA:Z:chrY,-20549275,59M67S,7;chrY,+19630445,67S59M,7;
D00691:39:C7HGRANXX:7:1313:10466:58327  353 chr10   94741   5    57H69M chr19   6502177 0   CACCGGTGGCTTCGTTGTAGTACACGTTGATGCGCTCCAGCTGGAGGTCGCTATCTCCGTGGTAAGTGC   FFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFF   NM:i:7  MD:Z:5C4C32C4G3G2C8G4   AS:i:34 XS:i:29 SA:Z:chr9,140136365,-,68S58M,52,4;  XA:Z:chrY,-20549265,69M57S,8;chrY,+19630445,57S69M,8;
D00691:39:C7HGRANXX:7:1301:9495:12136   97  chr10   94741   4    51S75M chr19   6502177 0   CCATGGTGCCGGGCTCCAAGTCCACGAGCACGGCGCGGGGCACATACTTGCCACCGGTGGCTTCGTTGTAGTACACGTTGATGCGCTCCAGCTGGAGGTCGCTATCTCCGTGGTAAGTGCCAGTGG  BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFF<<BFFFFFFF//BFFFFFFFFFFFFFFFFFFFFFBFFBFF  NM:i:8  MD:Z:5C4C32C4G3G2C8G7C2 AS:i:37 XS:i:32 SA:Z:chr9,140136365,-,74S52M,4,3;   XA:Z:chrY,+19630445,51S75M,9;chrY,-20549259,75M51S,9;   MQ:i:25
D00691:39:C7HGRANXX:7:2201:12400:93441  371 chr10   94741   6    64H61M chr9    140136365   0   CACCGGTGGCTTCGTTGTAGTACACGTTGATGCGCTCCAGCTGGAGGTCGCTATCTCCGTG   FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB   NM:i:6  MD:Z:5C4C32C4G3G2C5 AS:i:33 XS:i:28 SA:Z:chr9,140136365,+,60S65M,49,5;  XA:Z:chrY,+20549273,61M64S,7;chrY,-19630445,64S61M,7;
D00691:39:C7HGRANXX:7:2105:4071:100631  433 chr10   94741   8    76H50M chr9    140136947   0   CACCGGTGGCTTCGTTGTAGTACACGTTGATGCGCTCCAGCTGGAGGTCG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB  NM:i:4  MD:Z:5C4C32C4G1 AS:i:33 XS:i:28 SA:Z:chr9,140136365,+,49S77M,54,6;  XA:Z:chrY,+20549284,50M76S,5;chrY,-19630445,76S50M,5;
D00691:39:C7HGRANXX:7:2308:13827:14580  97  chr10   94765   0    48M77S chr19   6502177 0   CGTTGATGCGCTCCAGCTGGAGGTCGCTATCTCCGTGGTAAGTGCCAGTGGGATCAATGCCATGCTCGTCGCTGATTACCTCCCAGAACTTGGCGCCAATCTGGTTGCCGCACTGCCCAGCCTGC   BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFF<F/BFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFF   NM:i:5  MD:Z:19C4G3G2C8G7   AS:i:23 XS:i:23 XA:Z:chr4,+190905620,48M77S,5;chr9,-141069855,77S48M,5;chr18,+49150,48M77S,5;   MQ:i:25
D00691:39:C7HGRANXX:7:1209:11322:53678  99  chr10   95877   48   126M   =   96056   305 CCAGGCTTTTGGATTACCCAAACTGAGGAGTTATTTCTTCTGGTAAACATTTTTCAGATGGGGTGGGGAATGTCTCGATCTAACCAGTGAAGGTGTCAGTAAGCATTAGCAAATATTTGAATCTCC  BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFF  NM:i:2  MD:Z:0G71C53    AS:i:120    XS:i:115     XA:Z:chr16,-90159613,126M,3;chr4,+190906717,126M,5;chr18,+50253,126M,5;chrY,-9967205,126M,5;chr9,-141068669,126M,5;    MQ:i:60
D00691:39:C7HGRANXX:7:1209:11322:53678  147 chr10   96056   60   126M   =   95877   -305    CCTCAATTTTGGACAGGTTTAACTGGAGAAGGAGAAAATTGCTGGCCATTTGAGTCATGTCAGGCACAAAGCTCACAGGGCTGAGTCACCTGTTTTAGTGTCTTGAAAAGATTTACCCCTATAAAC  FFFFFFFFBFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB  NM:i:0  MD:Z:126    AS:i:126    XS:i:111     XA:Z:chr18,-50432,126M,3;chr9,+141068490,126M,4;chrY,+9967026,125M1S,4;chr16,+90159438,4S117M5S,3; MQ:i:48
D00691:39:C7HGRANXX:7:1110:2613:30476   99  chr10   116605  60   122M   =   116651  172 CCCAGTCTCTACTAAAAATACAATAATCAGCCAGGCATGGTGGCGCAGACCTGTAATCCCAGCTACTCAAGAGGCTGAGGACGAATTACTTGAACACAGGAGGTGGAGGCTGCAGTCAGCCG  BBBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFBBFFFFF NM:i:0   MD:Z:122    AS:i:122    XS:i:102    XA:Z:chr9,-141048001,122M,4;    MQ:i:60
D00691:39:C7HGRANXX:7:1110:2613:30476   147 chr10   116651  60   126M   =   116605  -172    AGACCTGTAATCCCAGCTACTCAAGAGGCTGAGGACGAATTACTTGAACACAGGAGGTGGAGGCTGCAGTCAGCCGAGATCTCCACTGCGCCACTGCACTCCAGCATGGGAGACAGAGCAGAACCC  B<FF/BFFF</FFFFFFBFFBFF<FFBFFFFFFFFFFFBFFFFFFFFFFFFF<FFFB<BFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBF<FFFFFFFFFBFFFFFFFFFFFBBBBB  NM:i:0  MD:Z:126    AS:i:126    XS:i:111     XA:Z:chr9,+141047951,126M,3;chr18,-70028,126M,4;   MQ:i:60
D00691:39:C7HGRANXX:7:1110:5694:99774   99  chr10   117523  60   39M1I17M   =   117654  257 TGCACTCCAGCCTGAGAAGAAAAAGTGAAAATCTGTCTCAAAAAAAAAAGTGGGGAG   BBBBB<FFFFFFFFFFFFFFFFFFFFF</</BFFFBBFF<<FFFB<BFFF<FFFFBF   NM:i:1  MD:Z:56 AS:i:49 XS:i:29 MQ:i:60
D00691:39:C7HGRANXX:7:1110:5694:99774   147 chr10   117654  60   126M   =   117523  -257    CCCAGGAGTTAAAGACAAACCTGAGGGACATAAAGATCCTGCTTAAATTAGCAGTGCATGGTGGCTGGTGCCTATAGTCCAAGCTACTTGGGAGGCTGAGGCAGGAGGATTGCTGGAGCCCAGGAG  BFBBB/BF/BFFFFFFFFFFFFBFFFFFFFFFFFFFBFFB/FBFFBF<FFFFFBBFFFFFFFBFF<B<FB/FFFFFBFFFFFFFFFBBFFFFFFB<FFFFFFFFFFFFFFFFBFBBFFFFFBBBBB  NM:i:0  MD:Z:126    AS:i:126    XS:i:101     XA:Z:chr18,-71035,126M,5;  MQ:i:60
D00691:39:C7HGRANXX:7:1108:3465:47458   147 chr10   119991  5    38S20M66S  =   119991  -20 TACAGCAGCCTGGATGGATTTGATCCACTCATCTTTCTCCTCCTGGGTGGGTGCTGAGATTCGGTACACCATGTGGTTCCCCTCCACTACCCGGCCGTCAGCCTCTGTTTTGCAGGCTTTGATG    FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB    NM:i:0  MD:Z:20 AS:i:20 XS:i:19 XA:Z:chr12,-54786996,31S19M74S,0;   MQ:i:5
D00691:39:C7HGRANXX:7:1108:3465:47458   99  chr10   119991  5    67S20M39S  =   119991  20  GCCAACATCTCATAGAAGGGGTCCACACTTACAGCAGCCTGGATGGATTTGATCCACTCATCTTTCTCCTCCTGGGTGGGTGCTGAGATTCGGTACACCATGTGGTTCCCCTCCACTACCCGGCCG  BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<  NM:i:0  MD:Z:20 AS:i:20 XS:i:19 XA:Z:chr12,+54786996,60S19M47S,0;   MQ:i:5
D00691:39:C7HGRANXX:7:1110:18049:20672  99  chr10   122194  60   125M   =   122356  288 CCACGTTCCTCCTCCTCTCCGGGGACCAGGGTCTCTCCCCAGAAACAAAATCGCATCGGTAACCGGCATCTTGTCCTGTGCTGGGGGTGAGCCGCCCAAGCCTCCATGAAGGGACGCTCGTACAA   BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFBFFFFFFFFFFFFFFFF   NM:i:0  MD:Z:125    AS:i:125    XS:i:105     XA:Z:chr18,+75600,125M,4;  MQ:i:60
D00691:39:C7HGRANXX:7:1110:18049:20672  147 chr10   122356  60   126M   =   122194  -288    GCCGCGCTCGCTCCGCTGCACTCACAGCGGCGGCAGGAAGCCTTTTTCTCACTTTCTCCCCGGCGGCCCCAGGTGTCCCGGAGCGTCTCCCTGTCCTCACAGCGGACGTGGCCCCAGGTGTCCCGA  <FFFFFFBFBFBFFFFFFFFFFFFFFFBFFFFFFFFFFFF<7/FFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB  NM:i:0  MD:Z:126    AS:i:126    XS:i:106     XA:Z:chr18,-75762,126M,4;  MQ:i:60
D00691:39:C7HGRANXX:7:1210:10697:93407  83  chr10   147812  5    23M100S    =   147812  -23 GGCAACAGAGGAGGGAAAGGAGATGATTTTCCCTGGTGGAAACGGATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGGGGCTGGTGTGGCTGCGGGG BFBFFFFFFFFFFFFFFFFF<FFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBBNM:i:1   MD:Z:2T20   AS:i:20 XS:i:0  MQ:i:5
D00691:39:C7HGRANXX:7:1210:10697:93407  163 chr10   147812  5    23M100S    =   147812  23  GGCAACAGAGGAGGGAAAGGAGATGATTTTCCCTGGTGGAAACGGATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGGGGCTGGTGTGGCTGCGGGG BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF<BFFFFFFFFFFFFFFFFFFFFFFFNM:i:1   MD:Z:2T20   AS:i:20 XS:i:0  MQ:i:5
D00691:39:C7HGRANXX:7:1209:19089:96642  83  chr10   147815  0    24S20M81S  =   147815  -20 GCTGGCCCTGGAGGAGATGGAGGCAACAGAGGAGGGAAAGGAGATGATTTTCCCTGGTGGAAACGGATGCAAAAGGGAGAATTTCCTTGGGACGACAAGGACTTCCGGAGCCTGGCTGTTTTGGG   FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB   NM:i:0  MD:Z:20 AS:i:20 XS:i:19 XA:Z:chrY,+13928508,79S19M27S,0;chr1,-180946205,28S19M78S,0;chr6,+40594269,78S19M28S,0; MQ:i:6
D00691:39:C7HGRANXX:7:1209:19089:96642  163 chr10   147815  6    56S20M50S  =   147815  20  ATTCAGTACCTCCAAAAAAAGAACCAAAAAATGCTGGCCCTGGAGGAGATGGAGGCAACAGAGGAGGGAAAGGAGATGATTTTCCCTGGTGGAAACGGATGCAAAAGGGAGAATTTCCTTGGGACG  BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  NM:i:0  MD:Z:20 AS:i:20 XS:i:0  MQ:i:0
D00691:39:C7HGRANXX:7:2101:5430:95369   99  chr10   153722  60   126M   =   153784  188 TAAAGACTTCTAAAATCTTGGGATGCAGCTGAGATTGCTATTTAAGTGGACAGAGCATTATAGGCCAGCTCCTTTGTGAGCTTCATACCCTACATGTGTGCTACTTTCAGCATGACCTGCCTCTAC  BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  NM:i:0  MD:Z:126    AS:i:126    XS:i:0  MQ:i:60
D00691:39:C7HGRANXX:7:2101:5430:95369   147 chr10   153784  60   126M   =   153722  -188    GGCCAGCTCCTTTGTGAGCTTCATACCCTACATGTGTGCTACTTTCAGCATGACCTGCCTCTACTTTTTGCAGGGGGACTACAATGTGGGTTTGGATGGCAAAAGCTCCTGGAGTGATTCCCTAGG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBBBB  NM:i:0  MD:Z:126    AS:i:126    XS:i:20 MQ:i:60
D00691:39:C7HGRANXX:7:2310:19944:26870  99  chr10   162451  0    39S19M17S  =   162451  19  GACACATCAACCATAGCCCAAAACAACAGGCAGCCCGGCAGCTGTTGCCCTCACTGTTGCCTATTACCTTGGGGG BBBBBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFF/FFFB/FB<FFFFFFFFFFFFBBFF NM:i:0  MD:Z:19 AS:i:19 XS:i:19 XA:Z:chr2,-217642450,11S19M45S,0;   MQ:i:0

产生.sam的命令即bowtie2的比对命令

mkdir -p  /home/vip41/reference/geneme
cd /home/vip41/reference/geneme
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gzip -d hg38.fa.gz
cat *.fa hg38

13、根据上面的命令，找到我使用的参考基因组 /home/jianmingzeng/reference/index/bowtie/hg38 具体有多少条染色体。
本题使用的命令：samtools view -H single/tmp.sorted.bam |awk '{print $2}'|cut -c4-9|sort -n|uniq -c|grep -v '_'
awk命令使用：
awk '{pattern + action}' {filenames}
pattern 表示 AWK 在数据中查找的内容，而 action 是在找到匹配内容时所执行的一系列命令。
awk工作流程是这样的：读入有'\n'换行符分割的一条记录，然后将记录按指定的域分隔符划分域，填充域，0则表示所有域,1表示第一个域,$n表示第n个域。默认域分隔符是"空白键" 或 "[tab]键"。
grep -v : 反转显示所有不满足查找模式的行

参考文章：AWK：https://www.cnblogs.com/ggjucheng/archive/2013/01/13/2858470.html
uniq: http://man.linuxde.net/uniq

vip41@VM-0-15-ubuntu:~/biosoft/data1/rmDuplicate/samtools$ samtools view -H single/tmp.sorted.bam |awk '{print $2}'|cut -c4-9|sort -n|uniq -c|grep -v '_'
      1 bowtie
      1 chr1
      1 chr10
      1 chr11
      1 chr12
      1 chr13
      1 chr14
      1 chr15
      1 chr16
      1 chr17
      1 chr18
      1 chr19
      1 chr2
      1 chr20
      1 chr21
      1 chr22
      1 chr3
      1 chr4
      1 chr5
      1 chr6
      1 chr7
      1 chr8
      1 chr9
      1 chrM
      1 chrX
      1 chrY
      1 1.0
vip41@VM-0-15-ubuntu:~/biosoft/data1/rmDuplicate/samtools$ samtools view -H single/tmp.sorted.bam |awk '{print $2}'|cut -c4-9|sort -n|uniq -c|grep -v '_'|wc
     27      54     365
去除前后两个，共25条染色体

14、上面的后缀为BAM 的文件的第二列，只有 0 和 16 两个数字，用 cut/sort/uniq等命令统计它们的个数。

vip41@VM-0-15-ubuntu:~/linux练习题/rmDuplicate/samtools/single$ samtools view tmp.sorted.bam |cut -f2|sort|uniq -c
     29 0
     24 16

15、重新打开 rmDuplicate/samtools/paired 文件夹下面的后缀为BAM 的文件，再次查看第二列，并且统计。

vip41@VM-0-15-ubuntu:~/linux练习题/rmDuplicate/samtools/paired$ samtools view tmp.sorted.bam | cut -f2|sort -n |uniq -c
      3 83
      2 97
      9 99
      8 147
      3 163
      1 323
      1 353
      1 371
      1 387
      1 433

16、下载 http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip 文件，并且解压，查看里面的文件夹结构， 这个文件有2.3M，注意留心下载时间及下载速度。

vip41@VM-0-15-ubuntu:~/linux练习题/rmDuplicate/samtools/paired$ wget http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip
--2018-12-14 23:25:52--  http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip
Resolving www.biotrainee.com (www.biotrainee.com)... 123.206.72.184
Connecting to www.biotrainee.com (www.biotrainee.com)|123.206.72.184|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2391084 (2.3M) [application/zip]
Saving to: ‘sickle-results.zip’

sickle-results.zi 100%[===========>]   2.28M   105KB/s    in 24s     

2018-12-14 23:26:17 (97.3 KB/s) - ‘sickle-results.zip’ saved [2391084/2391084]
vip41@VM-0-15-ubuntu:~/linux练习题/rmDuplicate/samtools/paired$ mv sickle-results.zip ~/linux练习题/
vip41@VM-0-15-ubuntu:~/linux练习题$ unzip sickle-results.zip 
Archive:  sickle-results.zip
   creating: sickle-results/
  inflating: sickle-results/command.txt  
  inflating: sickle-results/single_tmp_fastqc.html  
  inflating: sickle-results/single_tmp_fastqc.zip  
  inflating: sickle-results/test1_fastqc.html  
  inflating: sickle-results/test1_fastqc.zip  
  inflating: sickle-results/test2_fastqc.html  
  inflating: sickle-results/test2_fastqc.zip  
  inflating: sickle-results/trimmed_output_file1_fastqc.html  
  inflating: sickle-results/trimmed_output_file1_fastqc.zip  
  inflating: sickle-results/trimmed_output_file2_fastqc.html  
  inflating: sickle-results/trimmed_output_file2_fastqc.zip
vip41@VM-0-15-ubuntu:~/linux练习题$ cd sickle-results/
vip41@VM-0-15-ubuntu:~/linux练习题/sickle-results$ tree
.
├── command.txt
├── single_tmp_fastqc.html
├── single_tmp_fastqc.zip
├── test1_fastqc.html
├── test1_fastqc.zip
├── test2_fastqc.html
├── test2_fastqc.zip
├── trimmed_output_file1_fastqc.html
├── trimmed_output_file1_fastqc.zip
├── trimmed_output_file2_fastqc.html
└── trimmed_output_file2_fastqc.zip

0 directories, 11 files

17、解压 sickle-results/single_tmp_fastqc.zip 文件，并且进入解压后的文件夹，找到 fastqc_data.txt 文件，并且搜索该文本文件以 >>开头的有多少行？

vip41@VM-0-15-ubuntu:~/linux练习题/sickle-results$ unzip single_tmp_fastqc.zip 
Archive:  single_tmp_fastqc.zip
   creating: single_tmp_fastqc/
   creating: single_tmp_fastqc/Icons/
   creating: single_tmp_fastqc/Images/
  inflating: single_tmp_fastqc/Icons/fastqc_icon.png  
  inflating: single_tmp_fastqc/Icons/warning.png  
  inflating: single_tmp_fastqc/Icons/error.png  
  inflating: single_tmp_fastqc/Icons/tick.png  
  inflating: single_tmp_fastqc/summary.txt  
  inflating: single_tmp_fastqc/Images/per_base_quality.png  
  inflating: single_tmp_fastqc/Images/per_tile_quality.png  
  inflating: single_tmp_fastqc/Images/per_sequence_quality.png  
  inflating: single_tmp_fastqc/Images/per_base_sequence_content.png  
  inflating: single_tmp_fastqc/Images/per_sequence_gc_content.png  
  inflating: single_tmp_fastqc/Images/per_base_n_content.png  
  inflating: single_tmp_fastqc/Images/sequence_length_distribution.png  
  inflating: single_tmp_fastqc/Images/duplication_levels.png  
  inflating: single_tmp_fastqc/Images/adapter_content.png  
  inflating: single_tmp_fastqc/Images/kmer_profiles.png  
  inflating: single_tmp_fastqc/fastqc_report.html  
  inflating: single_tmp_fastqc/fastqc_data.txt  
  inflating: single_tmp_fastqc/fastqc.fo  
vip41@VM-0-15-ubuntu:~/linux练习题/sickle-results$ ls
command.txt     test2_fastqc.html
single_tmp_fastqc   test2_fastqc.zip
single_tmp_fastqc.html  trimmed_output_file1_fastqc.html
single_tmp_fastqc.zip   trimmed_output_file1_fastqc.zip
test1_fastqc.html   trimmed_output_file2_fastqc.html
test1_fastqc.zip    trimmed_output_file2_fastqc.zip
vip41@VM-0-15-ubuntu:~/linux练习题/sickle-results$ cd single_tmp_fastqc/
vip41@VM-0-15-ubuntu:~/linux练习题/sickle-results/single_tmp_fastqc$ ls
fastqc_data.txt  fastqc_report.html  Images
fastqc.fo    Icons           summary.txt
vip41@VM-0-15-ubuntu:~/linux练习题/sickle-results/single_tmp_fastqc$ cat fastqc_data.txt | grep '^>>'|wc -l
24

18、下载 http://www.biotrainee.com/jmzeng/tmp/hg38.tss 文件，去NCBI找到TP53/BRCA1等自己感兴趣的基因对应的 refseq数据库 ID，然后找到它们的hg38.tss 文件的哪一行。

vip41@VM-0-15-ubuntu:~/linux练习题$ wget http://www.biotrainee.com/jmzeng/tmp/hg38.tss
--2018-12-14 23:36:06--  http://www.biotrainee.com/jmzeng/tmp/hg38.tss
Resolving www.biotrainee.com (www.biotrainee.com)... 123.206.72.184
Connecting to www.biotrainee.com (www.biotrainee.com)|123.206.72.184|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2625188 (2.5M)
Saving to: ‘hg38.tss’

hg38.tss          100%[===========>]   2.50M   253KB/s    in 23s     

2018-12-14 23:36:29 (114 KB/s) - ‘hg38.tss’ saved [2625188/2625188]
vip41@VM-0-15-ubuntu:~/linux练习题$ cat hg38.tss | grep -n "NM_001276696"
22181:NM_001276696  chr17   7685550 7689550 1

19、解析hg38.tss 文件，统计每条染色体的基因个数。

vip41@VM-0-15-ubuntu:~/linux练习题$  cat hg38.tss |cut -f2|sort|uniq -c|grep -v '_'
   6050 chr1
   2824 chr10
   3449 chr11
   2931 chr12
   1122 chr13
   1883 chr14
   2168 chr15
   2507 chr16
   3309 chr17
    873 chr18
   3817 chr19
   4042 chr2
   1676 chr20
    868 chr21
   1274 chr22
   3277 chr3
   2250 chr4
   2684 chr5
   3029 chr6
   2720 chr7
   2069 chr8
   2301 chr9
      2 chrM
   2553 chrX
    414 chrY

20、解析hg38.tss 文件，统计NM和NR开头的熟练，了解NM和NR开头的含义。

vip41@VM-0-15-ubuntu:~/linux练习题$ cat hg38.tss |awk '{print$1}'|cut -c1-2|sort|uniq -c 
  51064 NM
  15954 NR

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