早教吧作业答案频道 -->其他-->
求生物信息学高手解答关于BOWTIE的一个问题!我现在正在使用BOWTIE软件,我遇到了一个非常大的难题,就是我想用一端碱基在我自己的一个数据库中比对,可是用你的话说:“Bowtie会根据indexes文
题目详情
求生物信息学高手解答关于BOWTIE的一个问题!
我现在正在使用BOWTIE软件,我遇到了一个非常大的难题,就是我想用一端碱基在我自己的一个数据库中比对,可是用你的话说:“Bowtie会根据indexes文件夹中建立的的e_coli的索引(.ebwt文件)快速的在e_coli的基因组中比对”,我把自己的数据库文件名称(如:TN1,是fasta格式已经拷到Index文件夹中了)写上去就提示:不能在index中找到数据库名为TN1的文件.请问要如何将数据库格式化啊?然后让它可以找到我的数据库文件?
我现在正在使用BOWTIE软件,我遇到了一个非常大的难题,就是我想用一端碱基在我自己的一个数据库中比对,可是用你的话说:“Bowtie会根据indexes文件夹中建立的的e_coli的索引(.ebwt文件)快速的在e_coli的基因组中比对”,我把自己的数据库文件名称(如:TN1,是fasta格式已经拷到Index文件夹中了)写上去就提示:不能在index中找到数据库名为TN1的文件.请问要如何将数据库格式化啊?然后让它可以找到我的数据库文件?
▼优质解答
答案和解析
用bowtie-build 将数据库格式化
Usage: bowtie-build [options]*
reference_in comma-separated list of files with ref sequences
ebwt_outfile_base write Ebwt data to files with this dir/basename
Options:
-f reference files are Fasta (default)
-c reference sequences given on cmd line (as )
-C/--color build a colorspace index
-a/--noauto disable automatic -p/--bmax/--dcv memory-fitting
-p/--packed use packed strings internally; slower, uses less mem
-B build both letter- and colorspace indexes
--bmax max bucket sz for blockwise suffix-array builder
--bmaxdivn max bucket sz as divisor of ref len (default: 4)
--dcv diff-cover period for blockwise (default: 1024)
--nodc disable diff-cover (algorithm becomes quadratic)
-r/--noref don't build .3/.4.ebwt (packed reference) portion
-3/--justref just build .3/.4.ebwt (packed reference) portion
-o/--offrate SA is sampled every 2^offRate BWT chars (default: 5)
-t/--ftabchars # of chars consumed in initial lookup (default: 10)
--ntoa convert Ns in reference to As
--seed seed for random number generator
-q/--quiet verbose output (for debugging)
-h/--help print detailed description of tool and its options
--usage print this usage message
--version print version information and quit
---------------------------------------------------
The pre-built E. coli index included with Bowtie is built from the sequence for strain 536, known to cause urinary tract infections. We will create a new index from the sequence of E. coli strain O157:H7, a strain known to cause food poisoning. Download the sequence file by right-clicking this link and selecting "Save Link As..." or "Save Target As...". The sequence file is named NC_002127.fna. When the sequence file is finished downloading, move it to the Bowtie install directory and issue this command:
bowtie-build NC_002127.fna e_coli_O157_H7
The command should finish quickly, and print several lines of status messages. When the command has completed, note that the current directory contains four new files named e_coli_O157_H7.1.ebwt, e_coli_O157_H7.2.ebwt, e_coli_O157_H7.rev.1.ebwt, and e_coli_O157_H7.rev.2.ebwt. These files constitute the index. Move these files to the indexes subdirectory to install it.
To test that the index is properly installed, issue this command:
bowtie -c e_coli_O157_H7 GCGTGAGCTATGAGAAAGCGCCACGCTTCC
If the index is installed properly, this command should print a single alignment and then exit.
Usage: bowtie-build [options]*
reference_in comma-separated list of files with ref sequences
ebwt_outfile_base write Ebwt data to files with this dir/basename
Options:
-f reference files are Fasta (default)
-c reference sequences given on cmd line (as )
-C/--color build a colorspace index
-a/--noauto disable automatic -p/--bmax/--dcv memory-fitting
-p/--packed use packed strings internally; slower, uses less mem
-B build both letter- and colorspace indexes
--bmax max bucket sz for blockwise suffix-array builder
--bmaxdivn max bucket sz as divisor of ref len (default: 4)
--dcv diff-cover period for blockwise (default: 1024)
--nodc disable diff-cover (algorithm becomes quadratic)
-r/--noref don't build .3/.4.ebwt (packed reference) portion
-3/--justref just build .3/.4.ebwt (packed reference) portion
-o/--offrate SA is sampled every 2^offRate BWT chars (default: 5)
-t/--ftabchars # of chars consumed in initial lookup (default: 10)
--ntoa convert Ns in reference to As
--seed seed for random number generator
-q/--quiet verbose output (for debugging)
-h/--help print detailed description of tool and its options
--usage print this usage message
--version print version information and quit
---------------------------------------------------
The pre-built E. coli index included with Bowtie is built from the sequence for strain 536, known to cause urinary tract infections. We will create a new index from the sequence of E. coli strain O157:H7, a strain known to cause food poisoning. Download the sequence file by right-clicking this link and selecting "Save Link As..." or "Save Target As...". The sequence file is named NC_002127.fna. When the sequence file is finished downloading, move it to the Bowtie install directory and issue this command:
bowtie-build NC_002127.fna e_coli_O157_H7
The command should finish quickly, and print several lines of status messages. When the command has completed, note that the current directory contains four new files named e_coli_O157_H7.1.ebwt, e_coli_O157_H7.2.ebwt, e_coli_O157_H7.rev.1.ebwt, and e_coli_O157_H7.rev.2.ebwt. These files constitute the index. Move these files to the indexes subdirectory to install it.
To test that the index is properly installed, issue this command:
bowtie -c e_coli_O157_H7 GCGTGAGCTATGAGAAAGCGCCACGCTTCC
If the index is installed properly, this command should print a single alignment and then exit.
看了 求生物信息学高手解答关于BO...的网友还看了以下:
A、B、C、D为短周期元素,在周期表中如图所示:A、C两种元素的原子核外电子数之和等于B原子的核电 2020-04-08 …
A、B、C为短周期元素,在周期表中如表所示:A、C两种元素的原子核外电子数之和等于B原子的核电荷数 2020-04-08 …
求两个2阶实矩阵AB使得A,B,(A+B)均可逆且(A+B)的逆等于A的逆加B的逆高等代数的题目 2020-04-12 …
A、B-、C、D、E、F都是含有18个电子的微粒(分子或单核离子),请回答:(1)A是单原子分子, 2020-05-12 …
B的最高价氧化物的水化物能和氢化物反应生成化合物甲问B是什么化合物甲是什么?B是短周期元素 2020-05-17 …
已知A的阳离子有2个电子层,1.8g的A原子与足量的稀硫酸反应,放出2.24L氢气,(标况下),A 2020-05-22 …
有A B 两种元素, 已知5.75g A的单质跟盐酸完全反应,在标况下产生2.8L氢气, 同时生成 2020-06-27 …
A在离篮4米处投篮,球的运行轨迹是抛物线,当球运行的水平距离为2.5米时,达到最高点高度为3.05 2020-07-05 …
(8分)A、B、C和D等4种元素,A元素所处的周期数、主族序数、原子序数均相等;B的原子半径是其所 2020-07-12 …
如图,在⊙O的内接△ABC中,∠ABC=30°,AC的延长线与过点B的⊙O的切线相交于点D,若⊙O 2020-07-19 …