Rsubread Annotation Files

  • Annotation files in Rsubread SAF format
  • Created from latest NCBI RefSeq GTF files
  • Gene IDs are NCBI Entrez Gene IDs
  • Chromosome names are in UCSC format
  • Files marked as "Strict" use only exons from "BestRefSeq" or "RefSeq" or "Cutated Genome" annotation sources. Gnomon and other computational gene models are excluded.
  • chrM added to chm13v2 T2T annotation using Johns Hopkins Liftoff annotation
  • PAR genes on chrY removed from mm39 and chm13v2.0 to avoid duplication of identical genes on the X and Y chromosomes

To use with Rsubread::featureCounts

  T2T <- read.delim("230321-chm13v2.0_RefSeqStrict.saf.gz")
  fc <- featureCounts(bamfiles, annot.ext=T2T, etc)

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