An EnrichmentKit is a lab method to enrich a sample for the DNA regions you are interested in. For instance an exome or custom gene capture kit, or amplicons.
EnrichmentKits are automatically created based on directories flowcells are detected in via scanning sequencing dirs, and entries in the sample_sheet
You need to upload:
- A Bed containing capture regions
- A GeneList containing symbols captured
If the canonical transcripts file contains only genes in the kit, you can turn it into a gene list via:
grep -v "^#" enrichment_kit.GeneTable.tsv | cut -f 1 > /tmp/gene_list.txt
Setup canonical transcripts (if this differs from existing canonical transcripts)
python3.8 manage.py import_canonical_transcript --genome-build=GRCh38 --annotation-consortium=RefSeq enrichment_kit.GeneTable.tsv
In Django admin, go to seqauto -> EnrichmentKits then select the kit.
Select the appropriate details for your kit (eg bed/genelist etc you uploaded) and click save.