How to choose Bowtie parameters?

Understand Your Data

• Identify the type of data you'll be aligning: DNA or RNA. Bowtie has parameters optimized for different types of data.

 

• Consider the quality and length of your reads; these factors may influence parameter settings.

Set Up Indexing Parameters

• Choose the appropriate reference genome for your project and build the Bowtie index using the bowtie-build command.

 

• Adjust the -a/--all parameter to define how many alignments are reported: high sensitivity may be necessary for projects where detecting all possible alignments is crucial.

Determine Alignment Strategy

• Decide whether to allow multiple alignments. Use the -k parameter to specify the number of reportable alignments for a read.

 

• Set the --best option if you require the best quality alignment rather than just the first valid match.

Configure Speed and Sensitivity

• Use the -n option to set maximum mismatches: a lower number increases accuracy, a higher number increases speed.

 

• For more refined searches in complex regions, adjust the -l/--seedlen parameter to set the length of the seed substrings used for alignment.

Control for Quality Filtering

• Use the --phred64 or --phred33 options as appropriate to define which Phred score version your data uses for input.

 

• Apply the -q option to work directly with reads that are in a quality-score-included format.

Handle Paired-End Reads

• If dealing with paired-end data, set the -I/--minins and -X/--maxins parameters to specify minimum and maximum fragment lengths.

 

• Specify the --fr/--rf/--ff options to indicate the orientation of your paired-end reads.

Perform Post-alignment Analysis

• Save logs or summary files using the --un and --al options to review unaligned and aligned reads for quality control.

 

• Consider exporting alignment results in SAM/BAM format using the -S option for compatibility with downstream analysis tools.