Linux command step by step

Below the statistics area shows the details of each process. First, to understand what the meaning of each column.

Press the corresponding letter to turn on / off the column, open capital letters, small letters closed.

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Linux command step by step

Under Linux ls command is one of the most commonly used commands. ls command is an abbreviation of the English word list, as the meaning of the English word list, its function is to list the contents of the specified directory and its associated attribute information. By ls command, you can view the file folder contains Linux, but you can view file permissions (including: directory, file permissions) to view the directory information.

02. Command Format

ls [option] . [file] .

03. Common Options

04. Reference Example

4.1 view the contents of the current directory

Only list the current directory files or directories, see other details, such as: file type, size, modification date and time, permissions, and links.

4.2 view the current directory and file attribute information

Use -l Option (lowercase L Character), details the file type, size, modification date and time, permissions, and hard links, etc. can be listed.

4.3 with easy-to-read format the output file size

The size of the file into a readable way, such as: 1G, 20M, 60K and so on. (If you are in K, can be used ls -lk ）

** Note: ** You can also use options —si ,with -h Similar, but —si 1000 bytes, and -h 1024 bytes (command: ls -l —si ）。

4.4 List all files in directories, including hidden files

4.5 display inode numbers for each file

4.6 Show full time

4.7 subdirectories recursively display

4.8 are listed in the file and color-coded markers

4.9 pairs of documents are classified according to special characters

4.10 listed by modification time of the file and folder details

4.11 sorted Modified

Catalog Details 4.12 display

UID and GID 4.13 print documents

4.14 All items separated by commas, and fill the entire width trekking

4.15 show details of the specified file

4.16 pairs directory plus symbol representing «/»

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Linux command step by step

We have already started using some directory-related commands, in fact, many Linux commands, but generally when in use will follow a certain format. For ease of use the command, we detailed description of the command format.

02. Command Prompt

Parsing the command prompt:

See in particular the following meaning of the fields in the above sentence.

[]: This is the prompt delimiter, no special meaning.

deng: displays the current logged-on user

@: Delimiter no special meaning.

localhost: The current short hostname of the system (the full name is the host localhost.localdomain).

: Represents the user’s current directory, the directory in this case the user is currently located is the home directory.

#: Command Prompt, Linux with user permission levels This symbol identifies login. If the super user, the prompt is #; If you are a regular user, the prompt is $.

03. user’s home directory

Linux system is a pure character interface, users log in, there must be a position of the initial login, this position is called the initial login user’s home: home directory super user’s home directory: / root. Average user’s home directory: / home / username.

Full user in their home directory, so we recommend performing experiments can be placed in the home directory. We look to switch the user directory, to see what works.

If you switch a user directory, the command prompt will become the user’s current directory is the last directory (do not show the full directory / usr / local / src, only the last directory src).

04. The basic format of the command

format:

command: executable file

Options: Used to adjust the command functions. Different commands, and the number of content options will be different; different command functions to be achieved, the number and content options will be different.

parameter: Object command is processed, usually can be a file name, directory, or a user name.

Tips: Command format [] on behalf of an option, that is, some commands can not write options or parameters, can be performed.

05. Role of options

Role option is to adjust the function commands.

After the ls command without options and parameters can be performed, but can only perform the most basic function, which displays the file name in the current directory.

If you add a «-l» option, you can see the contents displayed significantly increased. «-L» is a long format (long list) meaning, that is, detailed information about the file. As to the specific meaning of the «-l» option, we’ll explain in detail later. We can see the role of command option is to adjust the function. If there is no option, the command can only perform the most basic functions; and once there is an option, you can display richer data.

Linux options are divided intoShort-format options(-L) andLong format selectedItem (-all).

Short-format options are English shorthand, preceded by a — sign.

The long form of options is complete English word, with two front — No.

In general, short-format options is the abbreviation long form of options, which is a short-format options have corresponding long format options. Of course there are exceptions, such as short-format options -l ls command without a corresponding long format options. Therefore, the specific command options can later help us to learn commands to query.

06. effect parameters

Parameter is the operation target command, the general files, directories, users, and processes can be used as parameters command operations.

Object command who generally need to add parameters to specify the operation of the command Yes. If omitted, the default parameters generally.

The ls command does not specify the parameters behind, the default parameter is the current location, it will display the file name in the current directory.

07. Notes

Commands, command options, separated by a space between the command parameters.

When there are multiple command options can be combined. For example, you can ls -a / with ls -l / Merged into

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1 Send samples to get data

Send the sample to the sequencing company. The data obtained by NGS sequencing is raw data in fastq format. Usually, the sequencing company will do «clean» processing before returning the data to the customer, that is, get clean_data ; Regardless of whether there is clean or not, it is best to perform quality control; (The data returned by the company is a fastq.gz format compressed file for unidirectional sequencing, and two fastq.gz format compressed files for bidirectional sequencing)

2Quality control

2.1 Quality inspection

-o qc output results to folder qc (folder qc needs to be created in advance);

—noextract The default is to automatically decompress the output result. Adding —noextract to the command will not decompress, and the output result will be a *.zip file;
Or simpler, just use it without parameters:

After the detection is completed, you will get the sequencing result report *.html file (the *.zip compressed package above is the picture in the .html, which is useless), open the *.html file;

The option with a red X indicates that the quality inspection fails, which is the key to quality control;

For example, in the figure above Per base sequence content， It means to trim the first 15bp;

Such as Adapter Content, need to go to the connector;

2.2 Quality Control (QC) (Quality control of reads)

Quality Control, which means to filter low-quality reads. There are several types of low-quality reads:

• Reads containing Primer/Adaptor
• Reads with too many non-ATCG base N
• The number of bases with low sequencing quality is too high for reads

Software: NGSQC toolkit (Official website: http://www.nipgr.res.in/ngsqctoolkit.html; citation: http://journals.plos.org/plosone/article?id =10.1371/journal.pone.0030619)

The decompressed software includes 4 folders (QC Tools, Trimming Tools, Statistics Tools, Format-converter Tools) and 1 manual file in PDF format. The manual file is a detailed description; the 4 folders are all programs written in perl for QC. The order is determined according to its importance. The introduction is as follows:

QC Tools folder

QC Tools folder contains 5 perl programs: IlluQC.pl、 IlluQC_PRLL.pl (QC for offline reads on the ILLUMINA platform) and 454QC.pl, 454QC_PRLL.pl （ QC for offline reads on the 454 platform) and 454QC_PE.pl (for paired-end sequencing on the 454 platform) Off-machine reads QC); where IlluQC_PRLL.pl、 454QC_PRLL.pl and IlluQC.pl、 454QC.pl compared There is not much difference, but the addition of the ‘-c’ parameter is used for parallel calculation, which increases the program speed and is preferred.

By default, reads containing primer/adaptor and low-quality reads are removed, and statistical results and 6 graphical results are given.

perl . /NGSQCToolkit_v2.3.3/QC/IlluQC_PRLL.pl -pe . /Sample_1.fastq Sample_2.fastq 2 5 -c 4 -p 8 -l 70 -s 20 -o output

5 According to the sequencing machine version 1.8 and later, select 5;
-c 8 Choose 8 cpu, the more the faster;
-l 70 -s 20 Remove the low-quality bases whose base quality is lower than 20 (q20) in the data; (‘-l’ parameter) Low-quality bases are in reads The proportion >30% is low-quality reads;
-o selects the output folder

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Linux command step by step

netstat commandFor displaying various network-related information, such as network connection, routing tables, interface (Interface Statistics), masquerade connections, multicast membership (Multicast Memberships) and the like.

Overall, netstat output can be divided into two parts: one is the Active Internet connections, called an active TCP connection, where «Recv-Q» and «Send-Q» refers to% 0A the receive queue and transmitted queue. These numbers are generally should be zero. If not, it means the package is in the queue accumulation. This situation can only be seen in a very few cases; the other is Active UNIX domain sockets, called active Unix domain sockets (socket and the same network, but only for the native communication, a performance can be improved times).

02. Command Format

03. Common Options

04. Reference Example

4.1 List all ports (including listening and not listening)

4.2 List all TCP ports

4.3 List all UDP ports

4.4 routing table information

4.5 display list of network interfaces

4.6 TCP port displays connected, and PID

4.7 displays the current user UDP port, direct use IP

4.8 display multiple broadcast function group members

4.9 displays only the listening port

4.10 only lists all listening tcp ports

4.11 only lists all the listening udp port

4.12 only lists all the listening port UNIX

4.13 displays statistics for all ports

4.14 display statistics of TCP port

4.15 Display statistics of UDP ports

4.16 PID and process name displayed in the netstat output

netstat -p Can be used in conjunction with other switches, you can add «PID / process name» to netstat output, such debugging when you can easily find a specific port to run the program.

4.17 digital display port number, but it does not affect the resolution of host or user names

4.18 displayed in digital form but does not affect the host port or user name resolution

4.19 digital display of a user ID, but it does not affect the host and port name resolution

4.20 continuous display network information

4.21 display system does not support the address family

4.22 Display the routing information

4.23 Find network status information for the specified process

4.24 Find specify the port process

4.25 shows all network interface information

4.26 View IP address to connect up to a service ports

4.27 View port 3306 (mysql) is the number of links

4.28 TCP connection statistics

4.29 TCP statistics various states

Use uniq -c state statistics after 4.30 taken out after all sorts

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