Wikiomics:Staden - Revision history

Darek Kedra: Ubuntu ver 1.7.0 problems

2008-07-08T14:16:29Z

Ubuntu ver 1.7.0 problems

←Older revision		Revision as of 14:16, 8 July 2008
Line 75:		Line 75:
	* saving copies of database		* saving copies of database
	* saving consensus as Fasta/exp files		* saving consensus as Fasta/exp files
		+
		+
		+	=Version 1.7.0 on Ubuntu Linux=
		+	Simple downloading and unpacking does not produce working Staden installation on Ubuntu.
		+	For a fix see DrOlaf post [http://ubuntuforums.org/archive/index.php/t-696449.html here]

	== Credits ==		== Credits ==

Darek Kedra: /* Start up */

2008-05-06T14:48:20Z

Start up

←Older revision		Revision as of 14:48, 6 May 2008
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	source $STADENROOT/staden.login		source $STADENROOT/staden.login

-	/usr/biosoft/packages~~/staden~~/staden/current/	+	IMPERIAL:
		+	setenv STADENROOT /usr/biosoft/packages/staden/current/

Torsten Waldminghaus: add tags

2008-03-04T10:16:47Z

add tags

←Older revision		Revision as of 10:16, 4 March 2008
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	{{stub}}		{{stub}}
		+
		+	[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]]

Darek Kedra: + credits

2007-11-23T22:07:11Z

+ credits

←Older revision		Revision as of 22:07, 23 November 2007
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	* saving consensus as Fasta/exp files		* saving consensus as Fasta/exp files

		+	== Credits ==

		+	{{credits}}
		+
		+	* [[User:Darked\|Darek Kedra]] wrote this tutorial
		+	<!-- other contributors, put yourself here -->

	{{stub}}		{{stub}}

Bill Flanagan at 05:24, 20 November 2007

2007-11-20T05:24:17Z

←Older revision		Revision as of 05:24, 20 November 2007
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-	'''Staden''' - program package for DNA sequence assembly. It handles all steps from sequence pre-processing, through assembly, editing and finishing. Suitable for both small and very large sequence projects. Along [[Consed]] used in many leading DNA sequencing centers. Excellent contig editor in gap4.	+	'''Staden''' - program package for DNA sequence assembly. It handles all steps from sequence pre-processing, through assembly, editing and finishing. Suitable for both small and very large sequence projects. Along [[Wikiomics:Consed]] used in many leading DNA sequencing centers. Excellent contig editor in gap4.

	Executables for Linux, Windows, MacOS X and Solaris.		Executables for Linux, Windows, MacOS X and Solaris.

Bill Flanagan: 1 revision(s)

2007-11-20T04:01:06Z

1 revision(s)

←Older revision

Revision as of 04:01, 20 November 2007

Darked: /* Start up */

2007-02-07T16:25:41Z

Start up

New page

'''Staden''' - program package for DNA sequence assembly. It handles all steps from sequence pre-processing, through assembly, editing and finishing. Suitable for both small and very large sequence projects. Along [[Consed]] used in many leading DNA sequencing centers. Excellent contig editor in gap4.

Executables for Linux, Windows, MacOS X and Solaris.

Current version: 1.6.0 with 1.7.0 in the works.

==Program page==
http://staden.sourceforge.net/

==Sylabus==

===Start up===
* connecting to server using ssh and Exceed/Hummingbird
* setting staden environmental variables
before starting to work with Staden on Unix one has to set up environment

**tcsh
<pre>
setenv STADENROOT /path/to/your/staden/directory
source $STADENROOT/staden.login

/usr/biosoft/packages/staden/staden/current/

</pre>
**bash (Note '.' [dot] in the second line)
<pre>
export STADENROOT=/path/to/your/staden/directory
. $STADENROOT/staden.profile
</pre>
* basics of moving between directories, listing files etc. on Unix
<pre>
whoami
pwd
ls
ls *.exp
ls -l
ls -ltr
cd
cd directory_name
mkdir new_directory
</pre>

* viewing trace files with trev
<pre>
trev file_name.scf &
trev file_name.exp &
trev project1_file*.exp
</pre>

===Sequence preprocessing===
* data quality
* base calling
* vector(s) masking
* annotation of repeats
* starting pregap4
* setting up pregap4 run
* checking the results

===gap4===

* starting it
* menu options
* opening existing database/starting a new one
* contig editor
**trace display
**translation
**diff
**creating annotations
**searching/annotation searchin/offset searching
**breaking miss-assembled contigs
* Find internal joins function
* finding restriction sites
* saving copies of database
* saving consensus as Fasta/exp files

{{stub}}