SMAP target-selection

This is the manual for the SMAP utility tool SMAP target-selection of the SMAP package.

SMAP target-selection was designed to easily select groups of genes and create subsets of reference sequences as input for SMAP design and further downstream analysis with e.g. SMAP haplotype-sites, SMAP haplotype-window or SMAP effect-prediction.

SMAP target-selection extracts FASTA sequences from a reference genome sequence, using a short list of gene identifiers and/or grouping information, places candidate genes with the CDS encoded on the positive strand in the extracted reference sequence FASTA, and re-positions GFF features according to the novel coordinates, and may extract flanking regions of a user-defined length.

Contents:

• Scope & Usage
  • Scope
  • Integration in the SMAP workflow
  • Guidelines for the selection of reference sequences
  • Commands & options
  • Example commands
  • Output
• Feature Description
• How It Works
• Examples
  • Illustration
• Recommendations & Troubleshooting