Page Comparison

This page should serve as a reference for the many "things Linux" we use in this course. It is by no means complete – Linux is **huge** – but offers introductions to many important topics.

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• Macs and Linux have a Terminal program built-in
• Windows options:
  • Windows 10+
    • Command Prompt and PowerShell programs have ssh and scp (may require latest Windows updates)
      • Start menu → Search for Command
    • Putty – http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
      
      • simple Terminal and file copy programs
      • download either the Putty installer or just putty.exe (Terminal) and pscp.exe (secure copy client)
    • Windows Subsystem for Linux – Windows 10 Professional includes a Ubuntu-like bash shells
      • See https://docs.microsoft.com/en-us/windows/wsl/install-win10
      • We recommend the Ubuntu Linux distribution, but any Linux distribution will have an SSH client

Use ssh (secure shell) to login to a remote computers.

# General form:
ssh <user_name>@<full_host_name>

# For example
ssh abattenh@ls6.tacc.utexas.edu

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• ls *.bam – lists all files in the current directory that end in .bam
• ls [A-Z]*.bam – does the same, but only if the first character of the file is a capital letter
• ls [ABcd]*.bam – lists all .bam files whose 1st letter is A, B, c or d.
• ls *.{fastq,fq}.gz – lists all .fastq.gz and .fq.gz files.

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Streams and Piping

Standard streams and redirection

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• samtools view converts the binary small.bam file to text and writes alignment record lines one at a time to standard output.
  • -F 0x4 option says to filter out any records where the 0x4 flag bit is 0 (not set)
  • since the 0x4 flag bit is set (1) for unmapped records, this says to only report records where the query sequence did map to the reference
• | head -1000
  • the pipe connects the standard output of samtools view to the standard input of head
  • the -1000 option says to only write the first 1000 lines of input to standard output
    
• | cut -f 5
  • the pipe connects the standard output of head to the standard input of cut
  • the -f 5 option says to only write the 5th field of each input line to standard output (input fields are tab-delimited by default)
    
    • the 5th field of an alignment record is an integer representing the alignment mapping quality
    •  the resulting output will have one integer per line (and 1000 lines)
• | sort -n
  • the pipe connects the standard output of cut to the standard input of sort
  • the -n option says to sort input lines according to numeric sort order
  • the resulting output will be 1000 numeric values, one per line, sorted from lowest to highest
    
• | uniq -c
  
  • the pipe connects the standard output of sort to the standard input of uniq
  • the -c option option says to just count groups of lines with the same value (that's why they must be sorted) and report the total for each group
  • the resulting output will be one line for each group that uniq sees
  • each line will have the text for the group (here the unique mapping quality values) and a count of lines in each group
    

More Linux concepts

Environment variables

Environment variables are just like variables in a programming language (in fact bash is a complete programming language), they are "pointers" that reference data assigned to them. In bash, you assign an environment variable as shown below:

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