Examples

Illustration of SMAP effect-prediction

Below, we present a fictive example data set. The command to run SMAP effect-prediction is displayed with varying parameter settings to compare their respective output.

SMAP effect-prediction collects the following information from files prepared by the other modules of SMAP:

  1. the gene sequence from the reference genome; SMAP target-selection extracts the gene sequence and places it with the CDS on the + strand orientation in the reference FASTA file used for SMAP.

  2. the position of the CDS regions in the reference sequence; SMAP target-selection calculates the correct positions of the CDS with respect to the extracted gene reference sequence of 1).

  3. the position of the amplicon(s) in the gene reference sequence; SMAP design creates pairs of primers for HiPlex sequencing of genomic DNA, and stores the relative position of the corresponding border regions in a GFF file.

  4. the position of gRNA(s) for CRISPR/Cas genome editing within an amplicon; SMAP design optionally creates one or more gRNAs per amplicon to induce mutations in a particular position of the reference genome.

  5. the collection of haplotypes per locus and their relative frequencies per sample; SMAP haplotype-window extracts haplotypes (exact DNA sequences) using the exact same reference gene coordinates as outlined in 1)-4).

The user is advised to run SMAP effect-prediction first with the mandatory and default settings, and then decide on the most optimal parameter settings for your own design. The example data shown below are merely meant to illustrate the expected outcome of data sets processed with parameters adjusted to the specific species and reference (gene) sets. SMAP effect-prediction parameter settings are described in the section Commands & options.

Command used to run SMAP effect-prediction on a

smap effect-prediction haplotype_frequency.tsv genome.fasta borders.gff -a gene_features.gff -u guides.gff -p CAS9 -s 15 -r 20 -t 50 -e dosage -i diploid