These shell scripts were used for the procedure of remapping the Oryza sativa reference annotation, as found in RAP-DB in May 2018, to the new Carolina Gold genome assembly.

• prep_chrs.sh : prepares the per-chromosome data (indexed FASTA files with DNA and peptide sequences from the reference rice genome and its annotation)

• proc_chrs.sh : processes the per-chromosome data, transferring the annotation to the newly assembled Carolina Gold chromosome sequences; uses these other scripts from the gscripts parent directory (and repository):

  • paftools.js
  • gff_liftover.pl
  • gffcount
  • cds2rna_blat.pl

  These scripts also require other programs like gffread, cbdfasta/cdbyank, samtools, gmap, minimap2 and blat.