查看“Staden”的源代码

==pregap4==

<code>Files to process</code> - <code>add files</code> 添加所需要的ab1

<code>File</code> - <code>Load New Configure File</code> - configure

<code>Configure Modules</code> - <code>Run</code>

==gap4==

===一般拼接===

<code>File</code> - <code>New</code> 创建数据库

<code>Assembly</code> - <code>Normal shotgun assembly</code> 写以下内容

<code>Input reading filenames from</code> 选择 <code>file</code>

<code>List or file name</code> 选择 <code>pregap4</code> 生成的 <code>*.passed</code>文件

<code>Save failures to</code> 选择 <code>file</code>

<code>List or file name</code> 直接新建

<code>OK</code>

<code>File</code> - <code>Save consensus</code> - <code>normal</code>

<code>Select format</code> 选择 <code>fasta</code>

<code>Output file</code> 新建一个

<code>OK</code>

===再次拼接===

<code>View</code> - <code>Find internal joins</code>

或者

<code>View</code> - <code>Find repeats</code>

==trev==

<pre>trev ab1file</pre>
查看峰图

== configure ==
文件示例
 # Config file format version 1.0
 [module_list]
 set MODULE_PATH {$env(STADTCL)/pregap4/modules }
 set MODULES {
 	phred
 	atqa
 	eba
 	convert_trace
 	compress_trace
 	init_exp
 	augment_exp
 	quality_clip
 	sequence_vector_clip
 	cross_match_svec
 	screen_vector
 	polyA
 	cloning_vector_clip
 	screen_seq
 	blast
 	interactive_clip
 	repeat_masker
 	hetins
 	reference
 	mutscan
 	gap4_assemble
 	cap3_assemble
 	fakii_assemble
 	phrap_assemble
 	enter_assembly
 	email
 }
 
 [::init]
 set enabled 1
 set use_sample_name 0
 
 [::phred]
 set enabled 0
 
 [::atqa]
 set enabled 0
 
 [::eba]
 set enabled 1
 set scale logarithmic
 
 [::convert_trace]
 set enabled 1
 set down_scale 0
 set down_scale_range 255
 set output_format ctf
 set subtract_background 0
 set normalise 0
 set del_temp_files 1
 
 [::compress_trace]
 set enabled 0
 
 [::init_exp]
 set enabled 1
 
 [::augment_exp]
 set enabled 0
 
 [::quality_clip]
 set enabled 1
 set clip_mode confidence
 set offset 70
 set min_extent 0
 set max_extent 999999
 set min_length 0
 set window_length 50
 set conf_val 15
 set right_win_length 100
 set right_num_uncalled 5
 set left_win_length 25
 set left_num_uncalled 3
 
 [::sequence_vector_clip]
 set enabled 1
 set use_vp_file 1
 set vp_file /usr/bin/../share/staden/etc/vector_primer
 set vector_list {}
 set vp_length 40
 set min_5_match 60
 set min_3_match 80
 set def_5_pos -1
 
 [global_variables]
 set SF {}
 set SC {}
 set SP {}
 
 [::cross_match_svec]
 set enabled 0
 
 [::screen_vector]
 set enabled 0
 
 [::polyA]
 set enabled 0
 
 [::cloning_vector_clip]
 set enabled 0
 
 [::screen_seq]
 set enabled 0
 
 [::blast]
 set enabled 0
 
 [::interactive_clip]
 set enabled 1
 
 [::repeat_masker]
 set enabled 0
 
 [::hetins]
 set enabled 0
 
 [::reference]
 set enabled 0
 
 [::mutscan]
 set enabled 0
 
 [::gap4_assemble]
 set enabled 0
 
 [::cap3_assemble]
 set enabled 0
 
 [::fakii_assemble]
 set enabled 0
 
 [::phrap_assemble]
 set enabled 0
 
 [::enter_assembly]
 set enabled 0
 
 [::email]
 set enabled 0
 
 [::shutdown]
 set enabled 1
[[分类:Bioinformatics]]