來源：生信人的linux考試 http://www.bio-info-trainee.com/2900.html
一针炉、在任意文件夾下面創(chuàng)建形如 1/2/3/4/5/6/7/8/9 格式的文件夾系列。
vip21 08:29:21 ~/linux20
$ mkdir -p 1/2/3/4/5/6/7/8/9
vip21 08:33:46 ~/linux20
$ ls
1
vip21 08:34:05 ~/linux20
$ tree
.
└── 1
└── 2
└── 3
└── 4
└── 5
└── 6
└── 7
└── 8
└── 9
9 directories, 0 files
二、在創(chuàng)建好的文件夾下面屹电，比如我的是 /Users/jimmy/tmp/1/2/3/4/5/6/7/8/9 腔寡，里面創(chuàng)建文本文件 me.txt
三乐横、在文本文件 me.txt 里面輸入內(nèi)容:
Go to: http://www.biotrainee.com/
I love bioinfomatics.
And you ?
vip21 08:52:53 ~/linux20/1/2/3/4/5/6/7/8/9
$ cat > me.txt
Go to: http://www.biotrainee.com/
I love bioinfomatics.
And you ?
^C
vip21 08:53:51 ~/linux20/1/2/3/4/5/6/7/8/9
$ ls
me.txt
vip21 08:53:58 ~/linux20/1/2/3/4/5/6/7/8/9
$ cat me.txt
Go to: http://www.biotrainee.com/
I love bioinfomatics.
And you ?
四厦章、、刪除上面創(chuàng)建的文件夾 1/2/3/4/5/6/7/8/9 及文本文件 me.txt
vip21 08:54:37 ~/linux20/1/2/3/4/5/6/7/8/9
$ cd ~/linux20/
vip21 08:57:18 ~/linux20
$ rm -rf 1
vip21 08:57:41 ~/linux20
$ tree
.
0 directories, 0 files
五钮莲、在任意文件夾下面創(chuàng)建 folder1~5這5個文件夾免钻，然后每個文件夾下面繼續(xù)創(chuàng)建 folder1~5這5個文件夾
vip21 08:58:23 ~/linux20
$ mkdir -p folder{1..5}/folder{1..5}
vip21 08:59:36 ~/linux20
$ tree
.
├── folder1
│ ├── folder1
│ ├── folder2
│ ├── folder3
│ ├── folder4
│ └── folder5
├── folder2
│ ├── folder1
│ ├── folder2
│ ├── folder3
│ ├── folder4
│ └── folder5
├── folder3
│ ├── folder1
│ ├── folder2
│ ├── folder3
│ ├── folder4
│ └── folder5
├── folder4
│ ├── folder1
│ ├── folder2
│ ├── folder3
│ ├── folder4
│ └── folder5
└── folder5
├── folder1
├── folder2
├── folder3
├── folder4
└── folder5
六、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 臂痕，內(nèi)容也要一樣
vip21 09:02:30 ~/linux20
$ ls
folder1 folder2 folder3 folder4 folder5 me.txt
vip21 09:02:38 ~/linux20
$ echo folder{1..5}/folder{1..5}|xargs -n 1 cp me.txt
vip21 09:05:34 ~/linux20
$ tree
.
├── folder1
│ ├── folder1
│ │ └── me.txt
│ ├── folder2
│ │ └── me.txt
│ ├── folder3
│ │ └── me.txt
│ ├── folder4
│ │ └── me.txt
│ └── folder5
│ └── me.txt
├── folder2
│ ├── folder1
│ │ └── me.txt
│ ├── folder2
│ │ └── me.txt
│ ├── folder3
│ │ └── me.txt
│ ├── folder4
│ │ └── me.txt
│ └── folder5
│ └── me.txt
├── folder3
│ ├── folder1
│ │ └── me.txt
│ ├── folder2
│ │ └── me.txt
│ ├── folder3
│ │ └── me.txt
│ ├── folder4
│ │ └── me.txt
│ └── folder5
│ └── me.txt
├── folder4
│ ├── folder1
│ │ └── me.txt
│ ├── folder2
│ │ └── me.txt
│ ├── folder3
│ │ └── me.txt
│ ├── folder4
│ │ └── me.txt
│ └── folder5
│ └── me.txt
├── folder5
│ ├── folder1
│ │ └── me.txt
│ ├── folder2
│ │ └── me.txt
│ ├── folder3
│ │ └── me.txt
│ ├── folder4
│ │ └── me.txt
│ └── folder5
│ └── me.txt
└── me.txt
#另外一種解決方法（from 孫小潔老師）
for dirs in folder{1..5}/folder{1..5}; do cp me.txt $dirs; done
七伯襟，再次刪除掉前面幾個步驟建立的文件夾及文件
vip21 09:09:19 ~/linux20
$ ls
folder1 folder2 folder3 folder4 folder5 me.txt
vip21 09:09:20 ~/linux20
$ rm -rf folder*
vip21 09:10:28 ~/linux20
$ ls
me.txt
八、下載 http://www.biotrainee.com/jmzeng/igv/test.bed 文件握童，后在里面選擇含有 H3K4me3 的那一行是第幾行姆怪，該文件總共有幾行。
wget -c http://www.biotrainee.com/jmzeng/igv/test.bed
ls
cat test.bed | grep -n H3K4me3
cat test.bed | wc -l
九、下載 http://www.biotrainee.com/jmzeng/rmDuplicate.zip 文件稽揭，并且解壓俺附，查看里面的文件夾結(jié)構(gòu)
wget -c http://www.biotrainee.com/jmzeng/rmDuplicate.zip
ls
unzip rmDuplicate.zip
tree rmDuplicate
十、打開第九題解壓的文件溪掀，進(jìn)入 rmDuplicate/samtools/single 文件夾里面事镣，查看后綴為 .sam 的文件，搞清楚 生物信息學(xué)里面的SAM/BAM 定義是什么揪胃。
vip21 09:46:25 ~/linux20
$ cd ~/linux20/rmDuplicate/samtools/single/
vip21 09:47:56 ~/linux20/rmDuplicate/samtools/single
$ ls
readme.txt tmp.rmdup.bam tmp.sam tmp.sorted.vcf.gz
tmp.header tmp.rmdup.vcf.gz tmp.sorted.bam
vip21 09:48:04 ~/linux20/rmDuplicate/samtools/single
$ head tmp.sam
十一璃哟、安裝 samtools 軟件
conda軟件直接搜索，安裝即可喊递。
十二随闪、打開 后綴為BAM 的文件，找到產(chǎn)生該文件的命令骚勘。 提示一下命令是：
#查看BAM` 的文件
samtools view -h SRR1039508.hisat.bam
#查看命令
which samtools
十三題铐伴、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俏讹。
less -S hg38.fa |grep '^>' |sort |uniq -c |wc -l
十四題当宴、上面的后綴為BAM 的文件的第二列，只有 0 和 16 兩個數(shù)字泽疆，用 cut/sort/uniq等命令統(tǒng)計(jì)它們的個數(shù)户矢。
samtools view -h SRR1039508.hisat.bam | cut -f2 | sort | uniq -c
十五題、重新打開 rmDuplicate/samtools/paired 文件夾下面的后綴為BAM 的文件于微，再次查看第二列逗嫡，并且統(tǒng)計(jì)
samtools view tmp.sorted.bam | cut -f2|sort -n |uniq -c
十六題、下載 http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip 文件株依，并且解壓，查看里面的文件夾結(jié)構(gòu)延窜， 這個文件有2.3M恋腕，注意留心下載時間及下載速度。
wget -c http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip
unzip sickle-results.zip
tree sickle-results
十七題逆瑞、解壓 sickle-results/single_tmp_fastqc.zip 文件荠藤，并且進(jìn)入解壓后的文件夾，找到 fastqc_data.txt 文件获高，并且搜索該文本文件以 >>開頭的有多少行哈肖？
unzip single_tmp_fastqc.zip
cd single_tmp_fastqc/
cat fastqc_data.txt | grep -n '^>>' | wc -l
十八題、下載 http://www.biotrainee.com/jmzeng/tmp/hg38.tss 文件念秧，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淤井，然后找到它們的hg38.tss 文件的哪一行。
https://www.ncbi.nlm.nih.gov/gene/7157
wget -c http://www.biotrainee.com/jmzeng/tmp/hg38.tss
cat hg38.tss | grep -n 'NM_007294'
十九題、解析hg38.tss 文件币狠，統(tǒng)計(jì)每條染色體的基因個數(shù)游两。
cat hg38.tss | awk '{print$2}' | cut -c 1-5 | sort |uniq -c
cat hg38.tss |cut -f2|sort|uniq -c|grep -v '_'
二十題、解析hg38.tss 文件漩绵，統(tǒng)計(jì)NM和NR開頭的熟練贱案，了解NM和NR開頭的含義。
cat hg38.tss | grep '^NM' | sort |wc -l
cat hg38.tss | grep '^NR' | sort |wc -l
