SGA2BED(1)

📦 version 1.5.5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ NAME ✨

sga2bed — ok so basically, it converts SGA format into BED format. That's it, that's the whole vibe, no cap. It's a User Command, iykyk. 💖

🌸 SYNOPSIS 🌸

sga2bed [options] [<] <SGA file|stdin>

So you either hand it an SGA file as an argument, or you pipe the good stuff in through stdin. And yes bestie, that literal < is just part of the fit, don't question her. 🎀

🧚 DESCRIPTION 🧚

This is version 1.5.5, and here's where the options live — like, all of them, we're not skipping any, periodt:

  • -d, --debug — produce Debug information. Not me reading the vibes, it literally tells you what's going on. 🔍
  • -h, --help — show this Help text. The classic. The moment. 🙈
  • -i, --db <path> — use <path> to locate the chr_NC_gi file. Default is $HOME/db/genome. 💅
  • -l, --readlen <len> — set the Read length <len>. Unoriented SGA files get extended by +/-<len>/2. ✨
  • -c, --score <score> — normalisation factor for the BED score field (that's the 5th one). Default: score=1. 🔥
  • -n, --norm <normf> — normalisation factor for the BED score field (that's the 7th one). Default: normf=1. 🌸
  • -e, --extend f1:F1[,f2:F2] — set SGA optional field(s) f1(,f2,...) to BED field(s) F1,(F2,..). Fields are specified by column numbers. Accepted BED field values are 4, 5, and 7. Except for BED field 5 (the score field), BED fields 4 and 7 can be used to set multiple extension values from SGA. Fields 5 and 7 convert into numerical values, whereas BED field 4 takes character strings as they are. 🦋
  • -r, --nohdr — BED format without the annotation track header lines. No header, no problem. 💀
  • -x, --expand — expand SGA lines into multiple BED lines. One becomes many, it's giving main character energy. 👑
  • --name <name> — set the name for the track name field. Default: name=SGA-feature. ⭐
  • --desc <desc> — set the track description field. Default: desc="ChIP-Seq Custom data". 🎀
  • --color <col> — define the track color in comma-separated RGB values. Default: 100,100,100. 🌈

And yeah, that's the assignment: Convert SGA format into BED format. Slay. 🫶

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. Respect the icon who wrote it, fr fr. 💜

That's the whole page bestie — sga2bed version 1.5.5, dated March 2020. Go forth and convert, mwah 💅

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