Question

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？万分感谢！！！！！！

Answer 1

用bowtie-build 将数据库格式化

Usage: bowtie-build [options]* <reference_in> <ebwt_outfile_base>
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 <seq_in>)
-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 <int> max bucket sz for blockwise suffix-array builder
--bmaxdivn <int> max bucket sz as divisor of ref len (default: 4)
--dcv <int> 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 <int> SA is sampled every 2^offRate BWT chars (default: 5)
-t/--ftabchars <int> # of chars consumed in initial lookup (default: 10)
--ntoa convert Ns in reference to As
--seed <int> 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.

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多谢！请问您懂大概内容吗？可不可以举个例子，用点中文解释一下啊？谢谢！我英文不太好。。。