Staden #
Staden 是处理 Sanger 测序的软件包组。
pregap4 #
Files to process
- add files
添加所需要的ab1
File
- Load New Configure File
- configure 文末
Configure Modules
- Run
gap4 #
File
- New
创建数据库
Assembly
- Normal shotgun assembly
写以下内容
Input reading filenames from
选择 file
List or file name
选择 pregap4
生成的 *.passed
文件
Save failures to
选择 file
List or file name
直接新建
OK
File
- Save consensus
- normal
Select format
选择 fasta
Output file
新建一个
OK
trev #
trev ab1file
查看峰图
configure file #
# 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