Find repeated sites

Builds a target-gene index and searches potential repeated sites.

Pipeline unit:

Task

Run this task

ASOkai run --task find-repeated-sites --config-file ./config.yaml

ASOkai resolves and schedules missing dependencies automatically. Existing valid outputs and configured input overrides are reused.

Steps

Pipeline unit	Details
create-target-gene	Type: Step Description: Creates a target gene, extracts target sites, and writes a region FASTA.
build-bowtie2-index	Type: Step Description: Builds a Bowtie 2 index directory from a FASTA reference.
identify-potential-repeated-sites	Type: Step Description: Searches potential repeated sites that each target site’s own gapmer still binds.

This task is the public entry in the Analyses catalog. Its identify-potential-repeated-sites child is an internal step; inspect it with asokai describe step identify-potential-repeated-sites.

This task prepares the data needed to find the genomic sites at which each target site repeats, for RNase H1 gapmer ASOs. create-target-gene supplies the target gene and its FASTA, build-bowtie2-index indexes that FASTA, and identify-potential-repeated-sites searches the sequences that each site’s own gapmer still binds.

Aligning those sequences against the index and counting the genomic hits per target site are not implemented yet, so the task stops after the search and exposes the index and the potential repeated sites.

The gene child reads its configuration like any create-target-gene run. Supply an existing path or a named run for a child’s input to use a different target.