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).

helmetpastoralSoftware and s/w Development

Dec 13, 2013 (3 years and 7 months ago)

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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: Irel
and).

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.

Indic
ate 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/C
ELanalysis_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
Tran
sfer 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/CELanal
ysis_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

l
s

list everything in directory

ls



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