bowtie_seq
bowtie_seq uses bowtie to map sequences in the stream against a specified index created with format_genome. Sequences can originate from a FASTA type entries or from Solexa or FASTQ type entries in which case the quality scores will be utilized.
The resulting records look like this:
STRAND: +
SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
Q_ID: test
REC_TYPE: BOWTIE
S_ID: chr2L
S_BEG: 9999
SEQ: GGAGGACAATGCAAAAAAGCTAAGAACAAA
DESCRIPTOR: 6:G>C
SEQ_LEN: 30
SCORE: 1
S_END: 10028
---
The key ´SCORE´ denotes how many time this hit was located, which can then be used for outputting BED entries with write_bed.
The key ´DESCRIPTOR´ describes mismatch information.
Bowtie must be installed for bowtie_seq to work. Read more about bowtie here:
http://bowtie-bio.sourceforge.net/index.shtml
... | bowtie_seq [options] -g <genome>
or
... | bowtie_seq [options] -i <index>
[-? | --help] # Print full usage description.
[-g <genome!> | --genome=<genome!>] # Choose target genome (instead of index).
[-i <string> | --index_name=<string>] # Choose target index (instead of genome).
[-m <uint> | --mismatches=<uint>] # Mismatches allowed (0-3) - Default=0
[-h <uint> | --max_hits=<uint>] # Max hits to report - Default=all
[-s <uint> | --seed_length=<uint>] # Seed length - Default=28
[-c <uint> | --cpus=<uint>] # Number of CPUs to use - Default=1
[-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.
In order to use bowtie_seq to map a stack of query sequences from a FASTA file to a specified genome previously formatted with format_genome to see availible genomes), do:
read_fasta -i query_sequences.fna | bowtie_seq -g hg18
In order to use bowtie_seq to map a stack of query sequences from a FASTQ file to a specified index previously created with create_bowtie_index, do:
read_fastq -i query_sequences.fq | bowtie_seq -i ~/my_index/myindex
In order to use bowtie_seq to map a stack of query sequences from a Solexa file, do:
read_solexa -i query_sequences.solexa | bowtie_seq -g hg18
The result can be written in BED format with write_bed:
... | bowtie_seq -g hg18 | write_bed -xo output.bed
Martin Asser Hansen - Copyright (C) - All rights reserved.
July 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
bowtie_seq is part of the Biopieces framework.