日韩成人狠狠艹,谁有日韩视频99

在任意文件夾下面創(chuàng)建 folder1~5這5個文件夾，然后每個文件夾下面繼續(xù)創(chuàng)建 folder1~5這5個文件夾

zy@VM-0-15-ubuntu:~/tmp$ mkdir -p folder_{1..5}/folder_{1..5}
zy@VM-0-15-ubuntu:~$ tree tmp
tmp
├── folder_1
│   ├── folder_1
│   ├── folder_2
│   ├── folder_3
│   ├── folder_4
│   └── folder_5
├── folder_2
│   ├── folder_1
│   ├── folder_2
│   ├── folder_3
│   ├── folder_4
│   └── folder_5
├── folder_3
│   ├── folder_1
│   ├── folder_2
│   ├── folder_3
│   ├── folder_4
│   └── folder_5
├── folder_4
│   ├── folder_1
│   ├── folder_2
│   ├── folder_3
│   ├── folder_4
│   └── folder_5
└── folder_5
    ├── folder_1
    ├── folder_2
    ├── folder_3
    ├── folder_4
    └── folder_5

在第五題創(chuàng)建的每一個文件夾下面都創(chuàng)建第二題文本文件 me.txt ，內(nèi)容也要一樣。

zy@VM-0-15-ubuntu:~$ vim txt.sh
#!/bin/bash
#
for i in {1..5};do
   cd ~/tmp/folder_$i
   for I in {1..5};do
      cd ~/tmp/folder_$i/folder_$I
      echo -e:"Go to: http://www.biotrainee.com/ \n I love bioinfomatics.\n And you ?">me.txt
   done
done
##按下Esc :wq
zy@VM-0-15-ubuntu:~$ tree tmp
tmp
├── folder_1
│   ├── folder_1
│   │   └── me.txt
│   ├── folder_2
│   │   └── me.txt
│   ├── folder_3
│   │   └── me.txt
│   ├── folder_4
│   │   └── me.txt
│   ├── folder_5
│   │   └── me.txt
│   └── me.txt
├── folder_2
│   ├── folder_1
│   │   └── me.txt
│   ├── folder_2
│   │   └── me.txt
│   ├── folder_3
│   │   └── me.txt
│   ├── folder_4
│   │   └── me.txt
│   ├── folder_5
│   │   └── me.txt
│   └── me.txt
├── folder_3
│   ├── folder_1
│   │   └── me.txt
│   ├── folder_2
│   │   └── me.txt
│   ├── folder_3
│   │   └── me.txt
│   ├── folder_4
│   │   └── me.txt
│   ├── folder_5
│   │   └── me.txt
│   └── me.txt
├── folder_4
│   ├── folder_1
│   │   └── me.txt
│   ├── folder_2
│   │   └── me.txt
│   ├── folder_3
│   │   └── me.txt
│   ├── folder_4
│   │   └── me.txt
│   ├── folder_5
│   │   └── me.txt
│   └── me.txt
└── folder_5
    ├── folder_1
    │   └── me.txt
    ├── folder_2
    │   └── me.txt
    ├── folder_3
    │   └── me.txt
    ├── folder_4
    │   └── me.txt
    ├── folder_5
    │   └── me.txt
    └── me.txt

#如何查看echo的幫助信息
/bin/echo --help

下載 http://www.biotrainee.com/jmzeng/igv/test.bed 文件，后在里面選擇含有 H3K4me3 的那一行是第幾行，該文件總共有幾行。

zy@VM-0-15-ubuntu:~/tmp$ wget -c http://www.biotrainee.com/jmzeng/igv/test.bed
zy@VM-0-15-ubuntu:~/tmp$ grep -n H3K4me3 test.bed 
8:chr1  9810    10438   ID=SRX387603;Name=H3K4me3%20(@%20HMLE);Title=GSM1280527:%20HMLE%20Twist3D%20H3K4me3%20rep2%3B%20Homo%20sapiens%3B%20ChIP-Seq;Cell%20group=Breast;<br>source_name=HMLE_Twist3D_H3K4me3;cell%20type=human%20mammary%20epithelial%20cells;transfected%20with=Twist1;culture%20type=sphere;chip%20antibody=H3K4me3;chip%20antibody%20vendor=Millipore;  222 .   9810    10438   0,226,255

zy@VM-0-15-ubuntu:~/tmp$ wc -l test.bed 
10 test.bed

下載 http://www.biotrainee.com/jmzeng/rmDuplicate.zip 文件，并且解壓，查看里面的文件夾結(jié)構(gòu)

zy@VM-0-15-ubuntu:~/tmp$ wget -c http://www.biotrainee.com/jmzeng/rmDuplicate.zip

zy@VM-0-15-ubuntu:~/tmp$ unzip rmDuplicate.zip 
zy@VM-0-15-ubuntu:~/tmp$ ls
rmDuplicate  rmDuplicate.zip  test.bed
zy@VM-0-15-ubuntu:~/tmp$ tree rmDuplicate
rmDuplicate
├── 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

進入 rmDuplicate/samtools/single 文件夾里面，查看后綴為 .sam 的文件，搞清楚生物信息學里面的SAM/BAM 定義是什么。

zy@VM-0-15-ubuntu:~$ cd ~/tmp/rmDuplicate/samtools/single
zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/single$ less -S tmp.sam

# sam文件是序列比對后的標準文件。bam文件是sam的二進制文件。bam所占的內(nèi)存比較小。sam包括頭部注釋信息和比對信息，比對信息每行12列，以tab健分割。每列含義：

打開后綴為BAM 的文件，找到產(chǎn)生該文件的命令。

zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/single$ samtools view tmp.rmdup.bam

zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/single$ ls
readme.txt  tmp.header  tmp.rmdup.bam  tmp.rmdup.vcf.gz  tmp.sam  tmp.sorted.bam  tmp.sorted.vcf.gz
# 找到tmp.header查看
zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/single$ tail -n 3 tmp.header 
@SQ SN:chrY LN:57227415
@SQ SN:chrY_KI270740v1_random   LN:37240
@PG ID:bowtie2  PN:bowtie2  VN:2.2.9    CL:"/home/jianmingzeng/biosoft/bowtie/bowtie2-2.2.9/bowtie2-align-s --wrapper basic-0 -p 20 -x /home/jianmingzeng/reference/index/bowtie/hg38 -S /home/jianmingzeng/data/public/allMouse/alignment/WT_rep2_Input.sam -U /tmp/41440.unp"
# 其中CL字樣處就是要找的命令

根據(jù)上面的命令，找到我使用的參考基因組 /home/jianmingzeng/reference/index/bowtie/hg38 具體有多少條染色體。

# 頭文件的 @SQ的注釋信息就是參考基因組的注釋信息。
zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/single$ grep -o -E "SN:chr[0-9]+|SN:chr[a-z A-Z]+" tmp.header|sort |uniq

zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/single$ grep -o -E "SN:chr[0-9]+|SN:chr[a-z A-Z]+" tmp.header|sort |uniq|wc -l
26

上面的后綴為BAM 的文件的第二列，只有 0 和 16 兩個數(shù)字，用 cut/sort/uniq等命令統(tǒng)計它們的個數(shù)。

zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/single$ samtools view tmp.rmdup.bam |cut -f 2 |sort -n |uniq -dc
     16 0
     12 16

重新打開 rmDuplicate/samtools/paired 文件夾下面的后綴為BAM 的文件，再次查看第二列，并且統(tǒng)計

zy@VM-0-15-ubuntu:~/tmp/rmDuplicate/samtools/paired$ samtools view tmp.rmdup.bam |cut -f 2 |sort -n |uniq -dc
      2 83
      2 97
      8 99
      7 147
      2 163

下載 http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip 文件，并且解壓，查看里面的文件夾結(jié)構(gòu)

zy@VM-0-15-ubuntu:~/tmp$ wget -c http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip

zy@VM-0-15-ubuntu:~/tmp$ ls -lh
total 2.4M
drwxrwxr-x 4 zy zy 4.0K Nov 12  2016 rmDuplicate
-rw-rw-r-- 1 zy zy 103K Nov 12  2016 rmDuplicate.zip
-rw-rw-r-- 1 zy zy 2.3M Oct  6  2016 sickle-results.zip
-rw-rw-r-- 1 zy zy 3.1K May 18  2017 test.bed

解壓 sickle-results/single_tmp_fastqc.zip 文件，并且進入解壓后的文件夾，找到 fastqc_data.txt 文件，并且搜索該文本文件以 >>開頭的有多少行？

zy@VM-0-15-ubuntu:~/tmp/sickle-results$ unzip single_tmp_fastqc.zip 

zy@VM-0-15-ubuntu:~/tmp/sickle-results$ cd single_tmp_fastqc/
zy@VM-0-15-ubuntu:~/tmp/sickle-results/single_tmp_fastqc$ ls
fastqc_data.txt  fastqc.fo  fastqc_report.html  Icons  Images  summary.txt

y@VM-0-15-ubuntu:~/tmp/sickle-results/single_tmp_fastqc$ grep ^\>\> fastqc_data.txt |cat -n
     1  >>Basic Statistics  pass
     2  >>END_MODULE
     3  >>Per base sequence quality pass
     4  >>END_MODULE
     5  >>Per tile sequence quality pass
     6  >>END_MODULE
     7  >>Per sequence quality scores   pass
     8  >>END_MODULE
     9  >>Per base sequence content fail
    10  >>END_MODULE
    11  >>Per sequence GC content   warn
    12  >>END_MODULE
    13  >>Per base N content    pass
    14  >>END_MODULE
    15  >>Sequence Length Distribution  warn
    16  >>END_MODULE
    17  >>Sequence Duplication Levels   pass
    18  >>END_MODULE
    19  >>Overrepresented sequences warn
    20  >>END_MODULE
    21  >>Adapter Content   pass
    22  >>END_MODULE
    23  >>Kmer Content  warn
    24  >>END_MODULE

下載 http://www.biotrainee.com/jmzeng/tmp/hg38.tss 文件，去NCBI找到TP53/BRCA1等自己感興趣的基因?qū)?yīng)的 refseq數(shù)據(jù)庫 ID，然后找到它們的hg38.tss 文件的哪一行。(https://www.ncbi.nlm.nih.gov/gene/7157)

NCBI Reference Sequences (RefSeq).png

點擊NM_001126113.2跳轉(zhuǎn)到新頁面

用genome brower來瀏覽.png

瀏覽界面.png

zy@VM-0-15-ubuntu:~/tmp$ grep NM_001126113 hg38.tss 
NM_001126113    chr17   7685550 7689550 1

解析hg38.tss 文件，統(tǒng)計每條染色體的基因個數(shù)。

zy@VM-0-15-ubuntu:~/tmp$ cat hg38.tss |head
NR_046018   chr1    9874    13874   0
NR_024540   chr1    27370   31370   1
NR_104148   chr7    64664083    64668083    0
NR_111960   chrX    44871175    44875175    0
NR_028458   chr14   92104621    92108621    1
NR_028459   chr14   92104621    92108621    1
NR_026818   chr1    34081   38081   1
NR_026820   chr1    34081   38081   1
NR_026822   chr1    34081   38081   1
NM_001005484    chr1    67091   71091   0

zy@VM-0-15-ubuntu:~/tmp$ cat hg38.tss |cut -f2 >chr.txt
zy@VM-0-15-ubuntu:~/tmp$ less chr.txt
wc -l chr.txt
wc -l chr2.txt 
less chr2.txt
zy@VM-0-15-ubuntu:~/tmp$ sort chr2.txt |uniq -dc
   6157 chr1
   2838 chr10
   3577 chr11
   3014 chr12
   1133 chr13
   1982 chr14
   2377 chr15
   2696 chr16
   3794 chr17
    883 chr18
   5880 chr19
   4090 chr2
   1692 chr20
    895 chr21
   1410 chr22
   3395 chr3
   2277 chr4
   2821 chr5
   5782 chr6
   2785 chr7
   2221 chr8
   2310 chr9
      2 chrM
     32 chrUn
   2561 chrX
    414 chrY

解析hg38.tss 文件，統(tǒng)計NM和NR開頭的序列，了解NM和NR開頭的含義。

zy@VM-0-15-ubuntu:~/tmp$ grep -o -E "NM|NR" hg38.tss |sort |uniq -dc
  51064 NM
  15954 NR
# NM指的是轉(zhuǎn)錄組產(chǎn)物的序列; NR指的是非編碼的轉(zhuǎn)錄子序列

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