Difference between revisions of "Bowtie"
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bowtie-build NC_002127.fna e_coli_O157_H7 | bowtie-build NC_002127.fna e_coli_O157_H7 | ||
| − | + | <ins>Explanation</ins>: | |
| + | * '''bowtie-build''' is indexing creation tol of bowtie | ||
| + | * in this example '''NC_002127.fna''' is our reference and is the first argument | ||
| + | * the second argument is a label for the output index files, in this case '''e_coli_O157_H7''' | ||
| + | * The extensions of the output files will have the extension '''ebwt'''. The root name will be the label mentioned above with some changing added characters. | ||
Revision as of 12:02, 15 November 2016
Introduction
This article refers to the early version of bowtie, which in fact has a few features that version 2 does not have, such as colorspace data processing
Indexing the reference
This is done using the bowtie-build command and the input reference with the second argument being a label for the output files. It is an easy command, no options are required. Here is an example:
bowtie-build NC_002127.fna e_coli_O157_H7
Explanation:
- bowtie-build is indexing creation tol of bowtie
- in this example NC_002127.fna is our reference and is the first argument
- the second argument is a label for the output index files, in this case e_coli_O157_H7
- The extensions of the output files will have the extension ebwt. The root name will be the label mentioned above with some changing added characters.
