Skip to content

Instantly share code, notes, and snippets.

@bow

bow/bioinf-format-gotchas.md

Created April 5, 2017 20:05
Show Gist options
  • Save bow/f9a627699c92c7b82caf869bc2aaa5e6 to your computer and use it in GitHub Desktop.
Save bow/f9a627699c92c7b82caf869bc2aaa5e6 to your computer and use it in GitHub Desktop.
Download ZIP
Bioinformatics file format-specific quirks
Raw
bioinf-format-gotchas.md

GTF (http://mblab.wustl.edu/GTF22.html)

  • Coordinates are one-based, fully closed (i.e. position start at 1 and an interval's end position is included).
  • (for files released by GENCODE & Ensembl) CDS include start_codon but not stop_codon. stop_codon is included in the UTR instead.

refFlat (https://genome.ucsc.edu/FAQ/FAQformat.html)

  • Coordinates are zero-based, half open (i.e. position start at 0 and an interval's end position is not included).
  • (for refFlat.txt.gz file available via UCSC) CDS does include start and stop codons
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment