BED2SGA(1)

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

🎀 NAME 🎀

okay bestie, say hi to bed2sga — it's the little icon that takes your BED format and converts it into SGA format. that's it, that's the whole job, and it does it flawlessly. 💅

✨ SYNOPSIS ✨

bed2sga [options] [-s <s_assembly (e.g. hg19)>] [<] <BED file|stdin>

🦋 DESCRIPTION 🦋

so this is bed2sga version 1.5.5, and the options are literally right below this. no cap, go read them, they're giving main character energy. 👑

🌸 OPTIONS 🌸

  • -d, --debug — turns on the debug info. it spills the tea on what it's doing. 🫖
  • -h, --help — shows you this help text. your bestie when you're lost. 🫶
  • -i, --db <path> — use <path> to go find the assembly-specific chr_NC_gi file. the default is $HOME/db/genome, so if you didn't move anything, it already knows where to look. 📁
  • -f, --feature <ft> — sets the Feature name to <ft>. name it, slay it. ✨
  • -s, --species <spec> — sets the Assembly to <spec> (like hg19). yes, that -s from the synopsis. hi queen. 👋
  • -c, --center — generates a Centered SGA file. centered, balanced, thriving. 🧘
  • -u, --unoriented — generates an unoriented SGA file. it simply doesn't care about orientation and honestly? respect. 🙈
  • -r, --regional — generates a 2-line[+/-] SGA file that represents BED regions (think RepeatMasker regions). 🗺️
  • -e, --extend <f1,f2,...> — produces an extended SGA file with extra fields, specified by a comma-separated list of BED column numbers (from 1 to n). more columns, more drama. 💖
  • --useScore — uses the BED 'score' field (that's field #5) to set the SGA 'count' field. 🎯
  • --useSigVal — uses the BED 'Signal Value' field (that's field #7) to set the SGA 'count' field.
heads up bestie: this option is only valid for ENCODE narrowPeak. anywhere else and it's just not it. 🚫
  • --narrowPeak — use this one when you're working with ENCODE narrowPeak format.
real talk: with --narrowPeak, the options --useScore, -c, and -u are ignored. they get left on read. 💀

and yeah — convert BED format into SGA format. that's the whole vibe. 🌈

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫡

and that's a wrap, bestie — this was bed2sga version 1.5.5, dated March 2020, brought to you by the one and only User Commands era of BED2SGA(1). periodt. 💅✨

📦 where this page comes from