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- 17:51, 28 April 2017 (diff | hist) . . (+2,440) . . Samtools
- 00:07, 28 April 2017 (diff | hist) . . (+103) . . Qualimap (current)
- 00:01, 28 April 2017 (diff | hist) . . (+937) . . Qualimap
- 15:40, 26 April 2017 (diff | hist) . . (+185) . . Qualimap
- 15:36, 26 April 2017 (diff | hist) . . (+234) . . N Qualimap (Created page with "= Introduction = Inspecting bam files for quality = Installation = Has a number of dependencies: * optparse (available from CRAN) * NOISeq, Repitools, Rsamtools, GenomicFe...")
- 15:09, 26 April 2017 (diff | hist) . . (+217) . . Samtools
- 12:00, 26 April 2017 (diff | hist) . . (+16) . . Main Page
- 23:38, 19 April 2017 (diff | hist) . . (+966) . . N Hdi2u S25 (Created page with "= Accessing a running program or working with others interactively = * If you just run a job and then close down the terminal you ran it from, normally the job will be termin...") (current)
- 23:38, 19 April 2017 (diff | hist) . . (+538) . . N Hdi2u S24 (Created page with "= Processes = * Sometimes a command or program you run in the terminal goes on too long, or is obviously doing something you did not plan. * If there is no obvious way (such...") (current)
- 23:38, 19 April 2017 (diff | hist) . . (+385) . . N Hdi2u S23 (Created page with "= Environment Variables = * We have seen that the way commands run can be modified by the options passed on the command line. * One of the most important variables is PATH. T...") (current)
- 23:37, 19 April 2017 (diff | hist) . . (+793) . . N Hdi2u S22 (Created page with "* Try the command: grep "^DE" hsy14768.embl and grep -x "DE.*" hsy14768.embl * What are the <code>^</code> symbol and the <code>-x</code> parameter in these commands doing? *...") (current)
- 23:37, 19 April 2017 (diff | hist) . . (+830) . . N Hdi2u S21 (Created page with "= Grep = * grep stands for "global regular expression print" * you use this command to search for text patterns in a file, for example, Linux's mini-dicitonary. grep "adge"...") (current)
- 23:36, 19 April 2017 (diff | hist) . . (+262) . . N Hdi2u S20 (Created page with "= Piping output between applications = * <code>|</code>, often called an operator because it's so powerful * not always easy to find on the keyboard == Exercise == * "Pipe" t...") (current)
- 23:36, 19 April 2017 (diff | hist) . . (+1,235) . . N Hdi2u S19 (Created page with "= Removing files and directories = * The key difference between deleting something from the command line and using the graphical file browser is that in the first case the fi...") (current)
- 23:36, 19 April 2017 (diff | hist) . . (+352) . . N Hdi2u S18 (Created page with "= Linking to files = * copying big files can exhaust hard disk quickly. * You can instead create a link to it with the <code>ln -s</code> command. ln -s current.file linktoc...") (current)
- 23:35, 19 April 2017 (diff | hist) . . (+1,381) . . N Hdi2u S17 (Created page with "= Copying files and directories = * The basic command used to copy files using the command line is <code>cp</code>. * At a minimum, you must specify two arguments: the name o...") (current)
- 23:35, 19 April 2017 (diff | hist) . . (+1,425) . . N Hdi2u S16 (Created page with "== Getting by in only normal mode == * movement keys, "w" jump via start of words; "e" jump via ends; "fc" jump to next c * "0" for start of line, "A" for end of line and int...") (current)
- 23:35, 19 April 2017 (diff | hist) . . (+1,203) . . N Hdi2u S15 (Created page with "= Text editing = * There are very many text editors, but one of the most powerful and dependable is <code>vi</code>. * It has a steep but tiny learning curve, which we hope t...") (current)
- 23:34, 19 April 2017 (diff | hist) . . (+648) . . N Hdi2u S14 (Created page with "== Remember the man pages == There are many command line options available for each of the above commands, as well as functionality we do not cover here. To read more about th...") (current)
- 23:34, 19 April 2017 (diff | hist) . . (+1,212) . . N Hdi2u S13 (Created page with "= Reading text files = * These are useful when you want to look at the contents of a file, but not edit it. * Among the most common of these commands are <code>cat</code>, <c...") (current)
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