OmicSoft RefGene model

From Array Suite Wiki

Jump to: navigation, search

RefGene Gene Model

OmicSoft builds our RefGene gene models on common genome builds, exporting from the UCSC Genome Browser "Table Browser" the "NM" and "NR" accessions (coding and non-coding transcripts).

  1. Gene Model data are exported for the specified species and genome, so coordinates are based on the UCSC BLAT alignment
  2. The track is "NCBI RefSeq"
  3. The Table is "UCSC RefSeq (refGene)
  4. Minimal fields are selected for export: "name" (usually transcript_id) and "name2 (usually gene_id)

After exporting the gene model as GTF, OmicSoft creates a new .gmodel2 file and makes the gene model available on, and the gene model will be available in the OmicSoft Studio interface.