Step by step linux commands

Step by step linux commands

The more command of the contents of a text file longer content (not in a complete-screen display) screen output, and supports positioned keywords in the display. As for the content of text file contents less is recommended to use the cat command to view

more commands, functions like cat, cat command is the entire file contents displayed on the screen from top to bottom. will be more user-friendly display page by page-by-page reading, and basic instruction is to press the space bar (space) started for the next show, press b will be back (back) a display, and there are search string. more command to read the file back from the front, so when you start to load the entire file.

02. Command Format

more [-dlfpcsu] [-num] [+/ pattern] [+ linenum] [file …]

03. Common Options

command

more text commands one screen, full screen after the stop, and the percentage of the file is a message given so far has been displayed at the bottom of the screen: —More—(XX%) , You can interact with the above command.

04. Reference Example

4.1 view file contents, press Enter to browse down

4.2 specifies the number of lines per screen display

Use Options -NUM , Specify the number of lines per screen display is here designated 5 lines.

4.3 from NUM lines beginning to show the first file

Use Options +NUM From Paper NUM lines began to show, here on display from line 8.

4.4 displayed from matching the search string STRING file location

Use Options +/STRING Find the file in the first line of «Unix» strings appear, and start from the front two rows where the display output.

4.5 Use in combination with a conduit

After the contents of a command output, if the content is too large, more can be used to display the page, and plumbing required | Combined.

4.6 multiple blank lines as a single line

File1 document content is displayed page by page, line places subject to continuous blank line blank line display

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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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Step by step linux commands

as commandGNU organization launched a compilation of language compiler that supports many different types of processors.

02. Command Format

03. Common Options

04. Reference Example

4.1 assembly files to generate a target file

05. Appendix

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Step by step linux commands

dmesg commandIt is used to check and control for the core ring buffer. kernel will boot information stored in the ring buffer. Your chance to see if the boot information, you can use dmesg to see. Information stored in the boot /var/log/dmesg File.

02. Command Format

03. Common Options

04. Reference Example

4.1 List all drivers loaded into the kernel

dmesg Equipment failure diagnostic command is very important. in dmesg Carried out with the help of command when the hardware is connected or disconnected operation, we can see the information detected or disconnected hardware. dmesg Command can be used in most operating systems based on Linux and Unix in.

4.2 lists all detected hardware

To display all of the kernel to the hard device, you can use the grep command to search sda Key words

4.3 log 10 before the line output command dmesg

4.4 dmesg command output the last 10 lines of the log

4.5 search for a specific string is detected hardware

Since the ‘dmesg’ output command is too long, in which the search for a particular string is very difficult. Therefore, it is necessary to filter out Involving ‘usb’ ‘dma’ ‘tty’ ‘memory’ of the string like log lines.grep command The ‘-i’ option to omit sensitive.

4.6 Empty dmesg log buffer

We can use the following command to clear the dmesg log. This command will clear the ring buffer dmesg log. But you can still view the logs stored in the ‘/ var / log / dmesg’ file. You will have to connect any device dmesg log output.

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Linux Windows Install Setup Configuration Project

Guides and help on using basic Linux commands & basic Unix commands with step-by-step example.

Step by step example using Linux basic commands & Unix basic commands.

W hen you talk about using Linux as Operating System, at least you need to know some of the basic Linux commands that could help you do the configurations, setup and manage your Linux box using the Linux shell (or command line interpreter).

T he reason this Linux basic commands step by step with example guide design like this is to explain more plainly what these Linux command could do, and easier for us to find a command that should be used to do a specific task. Below is some of the collection of Linux commands and Unix commands presented with step by step examples.

Basic Linux Commands Collection:

Linux rm command — Linux command to remove files or directories. Linux ‘rm’ command can be used to remove/delete file, directory, hidden file and hidden directory on Linux operating system.

Linux shred command — Remove files more securely, Linux `shred’ overwrites devices or files, to help prevent even very expensive hardware from recovering the data form your disk.

Linux pwd command — Print the current working directory. Linux ‘pwd’ command is used to display the directory that you are currently in or your working directory.

Linux chsh command — The Linux ‘chsh’ command is used to change login shell on Linux command prompt.

Linux stat command — The Linux ‘stat’ command is used to display file or filesystem status on Linux Fedora Core command prompt.

Linux alias command — Make a string of Linux command (long line of command) to be substituted for a simple word Linux command. Use the Linux alias command if you want to make log chain of command to be short command.

Linux cp command — Step by step on using cp command to copy files, folder, hidden file and hidden folder on Linux Fedora Core operating system.

Copy contents of directory include hidden file and hidden directory — step to copy all contents of directory including the hidden files and the hidden directory inside the directory.

Linux mv command — Using mv command to moving files and folder, the Linux mv command also can be use to rename the files or directory in Linux system.

Linux mkdir command — To make an directories (some say folder) in Linux OS is relatively simple. The Linux command that usually involve on making directory usually mkdir command. The article show step by step on making the directory on bash command prompt using Linux mkdir command.

Make hidden directory — Making and using hidden directory with mkdir command.

Linux cat command — The cat is short form for ‘concatenate’ can be use to print the file contents to standard output, that is usually your PC screen. This article show the step by step on using the cat command to display the file contents on your Linux computer screen and show the step by step on how to create a file in your Linux box using the cat command.

Linux df command — To display the usage of Linux filesystem, the df command also display the statistic of free disk space and how much disk space that you already used on your Linux system and the df command also can be use to display the filesystem type mounted on the system.

Linux du command — The du command can be use to get information on the size of each file and directory in the system.

Linux rmdir command — Using ‘rmdir’ command to delete or remove empty directory/folder from Linux system.

Linux man command — Using ‘man’ command to get on line help or on line manual pages for Linux command.

Linux cd command — Change to another directory in Linux system using the cd command.

Linux date command — Get current system time and system date using date command.

Linux cal command — Display calendar with cal command.

Linux uname command — Get and Dispaly Linux System Information.

Lunux updatedb command — Update the database for locate command ( command that use to find files on Linux ) using the updatedb command.

Linux tree command — Display and view the Linux Fedora directory in the tree like format, the tree command also can be use to display directory inodes number and file inode number.

Linux shutdown command — The step by step example using shutdown command to shutdown Linux Fedora machine, reboot Linux fedora machine using shutdown command, shutdown Linux Fedora on specific time, and canceling shutdown process on Linux Fedora system.

Lunux ls command — The Linux ls command is usually use to view and list contents inside directory in Linux Fedora system. The ls command with -a option also can be use to list or show hidden file and hidden directory.

Note: All Unix and Linux basic commands used is execute on GNU/Linux Fedora Core using Bash shell on Computer Laboratory Test Project.

Keywords: basic linux command, linux command, linux basic, Unix command, basic unix command, info, rename, make directory, rm, shred, copy, pwd, chsh, alias, command, bash shell, mkdir, linux command example, fedora command

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