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• Setup directory for indexed target sequences. I used '$HOME/BOWTIE.idx'. After building reference DB, move them to this directory.
• Setup 'BOWTIE_INDEXES' as your environment variable. If you use bash (if you don't know, type 'echo $SHELL' at command-line), put the following line on your '~/.bashrc' file. Alternatively, you can use automation shell script as below.
• Naming convention (optional). If you want to analyze both normal base-space reads and color-space reads, it is good idea to discriminate both target DBs with a flag. I put '_c' at the end of DB name if it is prepared with '-C' option.

Color-space reads

• Prepare target(DB) sequence.

  Code Block
  $ bowtie-build -C <FASTA file> <DB name>

• Run bowtie. If you use fastq file (read sequences with quality scores),

  Code Block
  $ bowtie \-a \-C \-q \-t \--suppress 6 <DB name> <Query fastq filename> <output filename>

  If you want to ignore quality file, and use 'fasta' format reads,

  Code Block
  $ bowtie \-a \-C \-f \-t \--suppress 6 <DB name> <Query csfasta filename> <output filename>

Normal base reads

• Prepare target(DB) sequence.

  Code Block
  $ bowtie-build <FASTA file> <DB name>

• Run bowtie. If you use fastq file (read sequences with quality scores),

  Code Block
  $ bowtie \-a \-q \-t \--suppress 6 <DB name> <Query fastq filename> <output filename>

  If you want to ignore quality file, and use 'fasta' format reads,

  Code Block
  $ bowtie \-a \-f \-t \--suppress 6 <DB name> <Query csfasta filename> <output filename>

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I normally used the following bash script, after modifying each variable depending on data.

#\!/bin/bash
export BOWTIE_INDEXES="/home/taejoon/BOWTIE.idx/"
BOWTIE="/home/taejoon/src64/bowtie/bowtie-0.12.5/bowtie"
DB="DROME_E57_cdna_c"

QUERY="SRR034220.called.fastq"
OUT="SRR034220_called.$DB.bowtie_c"
time $BOWTIE \-a \-C \-q \-t \--suppress 6 $DB $QUERY $OUT

OUT="SRR034220_called.$DB.trim5_bowtie_c"
time $BOWTIE \-a \-C \-q \-t \--trim5 5 \--trim3 5 \--suppress 6 $DB $QUERY $OUT

Available on

Fourierseq

Phylocluster

User documentation

• To get started using bowtie, check out the bowtie manual.

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