Page Comparison

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• 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. $ bowtie-build <FASTA file> <DB name>
• Run bowtie. If you use fastq file (read sequences with quality scores), $ 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,$ bowtie -a -f -t --suppress 6 <DB name> <Query csfasta filename> <output filename>

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