linux答题软件_生信人的linux考试答题

在任意文件夹下面创建形如 1/2/3/4/5/6/7/8/9 格式的文件夹系列。

for i in `seq 9`;do a=${a}/$i;done;mkdir -p `pwd`$a

(base) yjk@DESKTOP-U8UULFU:~/test/1/2/3/4/5/6/7/8/9$ pwd

/home/yjk/test/1/2/3/4/5/6/7/8/9

在创建好的文件夹下面，比如我的是 /Users/jimmy/tmp/1/2/3/4/5/6/7/8/9 ，里面创建文本文件 me.txt

(base) yjk@DESKTOP-U8UULFU:~/test/1/2/3/4/5/6/7/8/9$ touch me.txt

在文本文件 me.txt 里面输入内容:

Go to: http://www.biotrainee.com/

I love bioinfomatics.

And you ?

(base) yjk@DESKTOP-U8UULFU:~/test/1/2/3/4/5/6/7/8/9$ vim me.txt

i

Go to: http://www.biotrainee.com/

I love bioinfomatics.

And you ?

Esc

:wq

Enter

删除上面创建的文件夹 1/2/3/4/5/6/7/8/9 及文本文件 me.txt

(base) yjk@DESKTOP-U8UULFU:~/test$ rm -rf 1/

在任意文件夹下面创建 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

(base) yjk@DESKTOP-U8UULFU:~/test$ for i in `seq 5`;do mkdir folder_$i;cd folder_$i;for j in `seq 5`;do mkdir folder_$j;done;cd ..;done

(base) yjk@DESKTOP-U8UULFU:~/test$ tree

.

├── 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

(base) yjk@DESKTOP-U8UULFU:~/test$ for i in `ls`;do cd $i;for j in `ls`;do cd $j;cat >me.txt<

Go to: http://www.biotrainee.com/

I love bioinfomatics.

And you ?

EOF

cd ../; done; cd ../; done

(base) yjk@DESKTOP-U8UULFU:~/test$ tree

.

├── folder_1

│ ├── folder_1

│ │ └── me.txt

│ ├── folder_2

│ │ └── me.txt

│ ├── folder_3

│ │ └── me.txt

│ ├── folder_4

│ │ └── me.txt

│ └── folder_5

│ └── me.txt

├── folder_2

│ ├── folder_1

│ │ └── me.txt

│ ├── folder_2

│ │ └── me.txt

│ ├── folder_3

│ │ └── me.txt

│ ├── folder_4

│ │ └── me.txt

│ └── folder_5

│ └── me.txt

├── folder_3

│ ├── folder_1

│ │ └── me.txt

│ ├── folder_2

│ │ └── me.txt

│ ├── folder_3

│ │ └── me.txt

│ ├── folder_4

│ │ └── me.txt

│ └── folder_5

│ └── me.txt

├── folder_4

│ ├── folder_1

│ │ └── me.txt

│ ├── folder_2

│ │ └── me.txt

│ ├── folder_3

│ │ └── me.txt

│ ├── folder_4

│ │ └── me.txt

│ └── folder_5

│ └── me.txt

└── folder_5

├── folder_1

│ └── me.txt

├── folder_2

│ └── me.txt

├── folder_3

│ └── me.txt

├── folder_4

│ └── me.txt

└── folder_5

└── me.txt

30 directories, 25 files

(base) yjk@DESKTOP-U8UULFU:~/test/folder_1/folder_1$ cat me.txt

Go to: http://www.biotrainee.com/

I love bioinfomatics.

And you ?

再次删除掉前面几个步骤建立的文件夹及文件

(base) yjk@DESKTOP-U8UULFU:~/test$ rm -rf *

(base) yjk@DESKTOP-U8UULFU:~/test$ wget http://www.biotrainee.com/jmzeng/igv/test.bed

(base) yjk@DESKTOP-U8UULFU:~/test$ vi test.bed

?H3K4me3

显示在第八行

总共有几行？

(base) yjk@DESKTOP-U8UULFU:~/test$ cat test.bed | wc -l

10

总共有10行

(base) yjk@DESKTOP-U8UULFU:~/test$ wget http://www.biotrainee.com/jmzeng/rmDuplicate.zip

(base) yjk@DESKTOP-U8UULFU:~/test$ unzip rmDuplicate.zip

(base) yjk@DESKTOP-U8UULFU:~/test$ tree rmDuplicate

rmDuplicate

├── picard

│ ├── paired

│ │ ├── readme.txt

│ │ ├── tmp.MarkDuplicates.log

│ │ ├── tmp.header

│ │ ├── tmp.metrics

│ │ ├── tmp.rmdup.bai

│ │ ├── tmp.rmdup.bam

│ │ ├── tmp.sam

│ │ └── tmp.sorted.bam

│ └── single

│ ├── readme.txt

│ ├── tmp.MarkDuplicates.log

│ ├── tmp.header

│ ├── 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

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

搞懂了，.sam是比对后的统计文件 ,不懂看这

(https://www.jianshu.com/p/9c99e09630da)

安装 samtools 软件

conda install -c bioconda samtools

打开 后缀为BAM 的文件，找到产生该文件的命令。 提示一下命令是：/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

(base) yjk@DESKTOP-U8UULFU:~/test/rmDuplicate/samtools/single$ samtools view tmp.sorted.bam | less

SRR1042600.42157053 0 chr1 629895 42 51M * 0 0 ATAACCAATACTACCAATCANTACTCATCATTAATAATCATAATGGCTATA CCCFFFFFHHHHHJJJJJJJ#4AGHJJIIJJIIIIIJJJJIJIIIIJJIJI AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:11C8A30 YT:Z:UU

SRR1042600.42212881 0 chr1 629895 42 51M * 0 0 ATAACCAATACTACCAATCANTACTCATCATTAATAATCATAATGGCTATA @@

SRR1042600.12010763 16 chr1 629895 24 51M * 0 0 ATAACCAATACTTCTAATCAAAACTCATCATTAATAATCATAATGGCTATA ?4B?1*4DD?11*1*?+22+<3F:3@EC:CC4EA,DEDDDDD?D3B:==+; AS:i:-10 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:11C0A1C6T29 YT:Z:UU

SRR1042600.29629551 16 chr1 629895 40 51M * 0 0 ATAACCAATACTACCAATCACTACTCATCATTAATAATCATAATGGCTATA HGF?JJHHFDHHGJJIHDFA+E?JIJJIIHGJJJJJJJHHHHHFFFFFCC@ AS:i:-8 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:11C8A30 YT:Z:UU

SRR1042600.41910745 0 chr1 629896 42 51M * 0 0 TAACCAATACTACCAATCAANACTCATCATTAATAATCATAATGGCTATAG CC@FFFFFHHHHGIIHIJJJ#3

SRR1042600.14329856 16 chr1 629896 8 18M1I32M * 0 0 AAACCAAATCCTCCAATCAAATCCTCATCATTAATAATCATAATGGCTATA #############################@IHHGCE9GHFHHHDDDDD

SRR1042600.15078214 16 chr1 629896 40 51M * 0 0 TAACCAATACTACCAATCAATACCCATCATTAATAATCATAATGGCTATAG 9?1EFDD4CE?1F@?F

SRR1042600.52533601 16 chr1 629896 40 51M * 0 0 TAACCAATACTACCAATCAATCCTCATCATTAATAATCATAATGGCTATAG D?0?*?1*?C?*EGC99>FA+3FBHBEBCA4HCC<:ffffff as:i:-8 xn:i:0 xm:i:2 xo:i:0 xg:i:0 nm:i:2 md:z:10c10a29 yt:z:uu>

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

这个我不会。。

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。

(base) yjk@DESKTOP-U8UULFU:~/test/rmDuplicate/samtools/single$ samtools view tmp.rmdup.bam | cut -f 2 | sort | uniq -c

16 0

12 16

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

(base) yjk@DESKTOP-U8UULFU:~/test/rmDuplicate/samtools/paired$ samtools view tmp.rmdup.bam | cut -f 2 | sort | uniq -c | sort -k 2n

2 83

2 97

8 99

7 147

2 163

1 323

1 353

1 371

1 387

1 433

(base) yjk@DESKTOP-U8UULFU:~/test$ wget http://www.biotrainee.com/jmzeng/sickle/sickle-results.zip

(base) yjk@DESKTOP-U8UULFU:~/test$ unzip sickle-results.zip

(base) yjk@DESKTOP-U8UULFU:~/test$ tree sickle-results

sickle-results

├── 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

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？

(base) yjk@DESKTOP-U8UULFU:~/test/sickle-results$ unzip single_tmp_fastqc.zip

(base) yjk@DESKTOP-U8UULFU:~/test/sickle-results$ cd single_tmp_fastqc/

(base) yjk@DESKTOP-U8UULFU:~/test/sickle-results/single_tmp_fastqc$ cat fastqc_data.txt | grep "^>>" | wc -l

24

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

(base) yjk@DESKTOP-U8UULFU:~/test$ wget http://www.biotrainee.com/jmzeng/tmp/hg38.tss

refseq搜tp53 human (https://www.ncbi.nlm.nih.gov/nuccore/?term=tp53+human+AND+srcdb_refseq%5BPROP%5D)找到任一人类tp53 的mRNA的accession号如NM_001276695

vi hg38.tss

?NM_001276695

8685行

退出即可

解析hg38.tss 文件，统计每条染色体的基因个数

(base) yjk@DESKTOP-U8UULFU:~/test$ cat hg38.tss | cut -f 2 | sort | uniq -c | sort -k 1n

1 chr11_KI270827v1_alt

1 chr17_GL000205v2_random

1 chr17_GL383566v1_alt

...

解析hg38.tss 文件，统计NM和NR开头的数量，了解NM和NR开头的含义。

(base) yjk@DESKTOP-U8UULFU:~/test$ cat hg38.tss | grep "^NR" | wc -l

15954

(base) yjk@DESKTOP-U8UULFU:~/test$ cat hg38.tss | grep "^NM" | wc -l

51064

或者这样

(base) yjk@DESKTOP-U8UULFU:~/test$ cat hg38.tss | grep -oE "^NR|^NM" | sort | uniq -c

51064 NM

15954 NR

NM代表mRNA

NR代表非编码的转录子序列，包括结构RNAs