Linux Analysis

16s Analysis

1.  Log onto server with your favorite SS file transfer software. (Both
    Client and File Transfer windows will be needed)

2.  Create new folder (directory) for the project within your directory
    using File Transfer window (example: Ireland).

3.  Transfer .CEL files to analyze to new folder using SSH File
    Transfer.

4.  Transfer param. file(s) to new folder.

5.  In gtldb2 Client window, change to new directory.

    a.  Type "cd", then \[space\]

    b.  Indicate path (Example: /auto/namib/jpmoberg/Ireland), then
        \[enter\]

6.  List everything in directory to check contents

    a.  Type "ls", then \[enter\]

7.  Run cel analysis program.

    a.  Indicate no-hangup by typing "nohup" then \[space\],

    b.  Indicate perl code by typing "perl" then \[space\],

    c.  Indicate path to analysis file location, then "/",

    d.  Indicate application name and version (.pl), then \[space\],

    e.  Type "-param_file", then \[space\],

    f.  Indicate parameter file name (.txt), then \[enter\]

Example:

juser@rapidserver:/auto/namib/juser/Ireland\> nohup perl
/usr2/people/shared/CELanalysis_64bit_Application/CELanalysis_v17.pl
-param_file run_params_using_subfamilies_limited.txt

Pathogen Specific Target Sequence Analysis

1.  Log onto server. (Both Client and File Transfer windows)

2.  Create new folder (directory) for the project within your directory
    using File Transfer window (example: Ireland).

3.  Transfer .CEL files to analyze to new folder using SSH File
    Transfer.

4.  In gtldb2 Client window, change to new directory.

    a.  Type "cd", then \[space\]

    b.  Indicate path (Example: /auto/namib/juser/Ireland), then
        \[enter\]

5.  List everything in directory to check contents

    a.  Type "ls", then \[enter\]

6.  Run program:

    a.  indicate path to analysis file location, then "/",

    b.  indicate application name (.pl), then \[space\],

    c.  indicate path to fasta file containing the target sequence, then
        "/",

    d.  indicate name of fasta file (.fasta) containing the target
        sequence (or prokMSA_id), then \[space\],

    e.  Type "\>" to redirect output to a new file, then \[space\],

    f.  Type desired name of output file then ".xls"

juser@rapidserver:/auto/namib/juser/Brucella\>
/auto/namib/shared/CELanalysis_64bit_Application/test_org_specific_PMs_against_their_MMs_v3.pl
/auto/namib/shared/Reference_Data/G2_path_specific_target_seqs/brucela.tabortus.dsuis.HaeIII_fasta.screen.Contig32.fasta
\> my_output.xls

Useful commands:

  -------------------- --------------------------------------------------
  pwd                  print working directory

  ls                   list everything in directory

  ls --lt              details, long list, sort by time

  cd                   change directory

  cp                   copy, list the path

  \*                   wild card, all similar

  .                    inside directory

  mkdir                make directory

  rm                   remove

  \[control\] c        stops program

  q                    quit file

  exit                 exit whole program

  ../                  go up one directory level

  top                  shows programs running

  less --s             sends info to screen, allow scrolling

  \[control\] z        suspend program to get a command prompt
  -------------------- --------------------------------------------------