COMPILESPLICECANDS(1)

📦
version 3.5.0 · 5 versions
, in ubuntu resolute, ubuntu stonking

✨ NAME ✨

compileSpliceCands — bestie, this lil icon finds introns by parsing a whole set of exon candidates that are sitting there in GFF format. 💅

🌸 SYNOPSIS 🌸

compileSpliceCands -f <splice candidates filename> -g <genome filename>

💖 OPTIONS 💖

🎀 Parameters:

  • -f <filename> — the potential splice sites, bestie, and they gotta be in gff format. 📄✨
  • -g <filename> — your genome file, and it has to be in fasta format. 🧬
  • -c <integer> — this one sets the number of potential splice sites that every potential splice site itself gets compared with. it's giving ✨comparison era✨ ngl.
  • -t <float> — has to be between 0 and 1 (no exceptions, she's strict 💀) and it defines how much the average coverage may differ. so like… tolerance vibes.
  • -m <integer> — defines how many bases around the splice site should be checked. it's giving personal space, but for bases. 🫶
  • -d — enables debugging output. turn this on when you wanna see everything she's thinking, main character energy fr fr. 🔍💅
  • -i <integer> — the maximum length an Intron can be. default is 500000, which, iykyk, is the human genome setting. 📏

👑 AUTHORS 👑

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. absolute legends, no cap, we stan. 🫶✨

📚 ADDITIONAL DOCUMENTATION 📚

okay so if you want the exhaustive documentation — and bestie, it is exhaustive — it lives right here:

/usr/share/doc/augustus/README.md.gz
go read it, it ate. 💖

and that's the whole page, bestie 🎀 — this one's from the AUGUSTUS manual, section 1 of the Unix manual pages (COMPILESPLICECANDS(1)), so yeah, section 1, first-section energy, iconic. now go compile some splice candidates and slay. 💅✨🦋

📦 where this page comes from