MANE Transcript Usage

Default behavior

  • For GRCh38 installs, PyFuse enables MANE resource generation by default.
  • For GRCh37 installs, MANE is skipped unless a custom MANE input is explicitly provided.

Why this matters

Official MANE resources are GRCh38-centered. Using MANE with GRCh37 usually implies back-mapped resources and should be treated carefully.

Reference: https://www.ncbi.nlm.nih.gov/refseq/MANE/

GRCh37 safety confirmation

If you provide --mane-file with --genome grch37, PyFuse:

  1. warns that MANE is GRCh38-centered
  2. asks for interactive yes/no confirmation
  3. skips MANE generation if you answer no

Output columns added by MANE

When MANE resource is available, PyFuse adds:

  • 5'_MANE_status
  • 3'_MANE_status
  • Gene_function

When MANE resource is unavailable, these fields are filled with ..