Introducing the Shell
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The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI.
Useful commands for navigating your file system include: ls , pwd , and cd .
Most commands take options (flags) which begin with a - .
Tab completion can reduce errors from mistyping and make work more efficient in the shell.
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Navigating Files and Directories
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The / , ~ , and .. characters represent important navigational shortcuts.
Hidden files and directories start with . and can be viewed using ls -a .
Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.
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Working with Files and Directories
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You can view file contents using less , cat , head or tail .
The commands cp , mv , and mkdir are useful for manipulating existing files and creating new directories.
You can view file permissions using ls -l and change permissions using chmod .
The history command and the up arrow on your keyboard can be used to repeat recently used commands.
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Redirection
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grep is a powerful search tool with many options for customization.
> , >> , and | are different ways of redirecting output.
command > file redirects a command’s output to a file.
command >> file redirects a command’s output to a file without overwriting the existing contents of the file.
command_1 | command_2 redirects the output of the first command as input to the second command.
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Writing Scripts
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Project Organization
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Sequences database creation
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There are other repositories other than NCBI
Useful command of this lesson is: makeblastdb .
The command takes options (flags) which begin with a - .
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Introducing to BLAST+ applications
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The BLAST+ package offers three categories of applications: 1.) search tools, 2.) BLAST database tools, and 3.) sequence filtering tools
The blastn, blastp, blastx, tblastx, tblastn, psiblast, rpsblast, and rpstblastn are considered search applications, as they execute a BLAST search
The makeblastdb, blastdb_aliastool, makeprofiledb, and blastdbcmd are considered BLAST database applications
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Trinity assembly
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Trinity assembles transcript sequences from Illumina RNA-Seq data
Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly
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Mapping
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Contig extention
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