![]() the -n option says to sort input lines according to numericsort order.the pipe connects the standard output of cutto the standard input of sort.the resulting output will have one integer per line (and 1000 lines).the 5th field of an alignment record is an integer representing the alignment mapping quality.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 pipe connects the standard output of headto the standard input of cut.the - 1000 option says to only write the first 1000 lines of input to standard output.the pipe connects the standard output of samtools view to the standard input of head.since the 0x4 flag bit is set ( 1) for unmappedrecords, this says to only report records where the query sequence did map to the reference.-F 0x4 option says to filter out any records where the 0x4 flag bit is 0 (not set).samtools view converts the binary small.bam file to text and writes alignment record lines one at a time to standard output.Samtools view -F 0x4 small.bam | head -1000 | cut -f 5 | sort -n | uniq -c # create a histogram of mapping quality scores for the 1st 1000 mapped bam records To see the difference between standard output and standard error try these commands: To redirect standard output and standard error to the same place, use the syntax 2 >&1.To redirect the standard error of a program you must specify its stream number using 2 >.since standard output is stream #1, this is the same as 1 >.a single > overwrites any existing target a double > appends to it.To take the standard output of a program and save it to a file, you use the > operator.When running batch programs and scripts you will want to manipulate standard output and standard error from programs appropriately. But they are separate streams, with different meanings. ![]() It is easy to not notice the difference between standard output and standard error when you're in an interactive Terminal session – because both outputs are sent to the Terminal. Standard streamsĮvery command and Linux program has three "built-in" streams: standard input, standard output and standard error. To avoid headaches, it is best not to create file/directory names with embedded spaces. While it is possible to create file and directory names that have embedded spaces, that creates problems when manipulating them. means "list contents of the parent directory." (two periods) means "directory above current." So ls. and you can use a hyphen ( - ) to specify a range of characters (e.g.brackets ( ) to allow for any character in the list of characters between the brackets.This technique is sometimes called filename globbing, and the pattern a glob. It matches "any length of any characters". * (asterisk) is the most common filename wildcard. The shell has shorthand to refer to groups of files by allowing wildcards in file names. Use Backspaceto remove text beforethe cursor Deleteto remove text afterthe cursor.Ctrl-right-arrow will skip by word forward Ctrl-left-arrow backward. Use Ctrl-e to jump the cursor to the endof the line.Use Ctrl-a (holding down the "control" key and "a") to jump the cursor to the beginningof the line.Right arrow and Left arrow move the cursor forward or backward on the current command line.The Down arrow "scrolls" forward from where you are in the command history.You can then edit them and hit Enter(even in the middle of the command) and the shell will use that command.Use Up arrow to retrieve any of the last 500 commands you've typed, going backwards through your history.work for shell commands too (like lsor cp).Tab twice – display all possible completions.if nothing shows up, there is no unambiguous match.single Tab – complete file or directory names up to any ambiguous part.On most modern Linux shells, Tab completion will: The Tab key is your best friend! Hit the Tab key once or twice - it's almost always magic! Hitting Tab invokes shell completion, instructing the shell to try to guess what you're doing and finish the typing for you. Type as little and as accurately as possible by using keyboard shortcuts! Tab key completion Getting around in the shell Important keyboard shortcuts ![]() ![]()
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