create_bowtie_index
Martin Asser Hansen edited this page Oct 2, 2015
·
6 revisions
create_bowtie_index creates a Bowtie index using ´bowtie-build´ on sequences found in the stream.
Bowtie must be installed in order for create_bowtie_index to work. Read more here:
http://bowtie-bio.sourceforge.net/index.shtml
... | create_bowtie_index [options] -d <my_dir> -i <my_index>
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-d <dir> | --directory=<dir>] # Directory to cantain index files.
[-i <string> | --index_name=<string>] # Index name.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
To create a bowtie index from a FASTA file, do:
read_fasta -i <FASTA file(s)> | create_bowtie_index -d ~/my_dir -i my_index -x
You will then get the following files:
~/my_dir/my_index.1.ebwt
~/my_dir/my_index.2.ebwt
~/my_dir/my_index.3.ebwt
~/my_dir/my_index.4.ebwt
~/my_dir/my_index.rev.1.ebwt
~/my_dir/my_index.rev.2.ebwt
And finally to use this new index with bowtie_seq, simply do:
read_fasta -i <FASTA file(s)> | bowtie_seq -i ~/my_dir/my_index
Martin Asser Hansen - Copyright (C) - All rights reserved.
July 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
create_bowtie_index is part of the Biopieces framework.