BED2BED_DISPLAY(1)

💖 BED2BED_DISPLAY 💖

okay bestie, so this is the manual for bed2bed_display from User Commands, and it is literally the glow-up station for your ChIP-seq peaks. sit down, grab a strawberry 🍓, and let's get into it.

✨ NAME ✨

bed2bed_display — the icon that converts a BED file into BED format that's actually suitable for displaying ChIP-seq peaks. no cap. 👑

🌸 SYNOPSIS 🌸

bed2bed_display [options] [-a <min BED score>] [-b <max BED score>] [<]
<BED file|stdin>

so you can hand it a file or just pipe stuff straight in from stdin, and the [<] thing is just chillin' there, minding its own business. 🫶

💅 DESCRIPTION 💅

version 1.5.5 — and here's where the options live, bestie:

🎀 OPTIONS 🎀

• -d, --debug — spill the tea and produce Debug information. 🐛
• -h, --help — show this Help text, i.e. the manual you're already reading. iconic behaviour.
• -f, --feature <ft> — set the Feature name to <ft>.
• -o, --oformat <1|2> — set the output Format. you got two choices and they are: 1 for BED (and yes that's the Default ✨) or 2 for BedGraph.
• --name <name> — set the name for the track name field. default is name=SGA-feature.
• --desc <desc> — set the track description field. default is desc="ChIP-Seq Custom data".
• --color <col> — define the track color as comma-separated RGB values. default is 100,100,100 (a very chill grey, ngl).
• --autoscale <on|off> — a data viewing parameter: turns auto-scale to UCSC data view on or off. default is OFF. 💤
• --always0 <on|off> — a data viewing parameter: always include zero. default is OFF.
• --wfunction <func> — a data viewing parameter: the windowing function. default is mean+whiskers|maximum|mean|minimum. pick your fighter. ⚔️
• --smoothing <grade> — a data viewing parameter: the smoothing window. default is OFF[0], and <grade> can be 0,2..16.
• --visibility <mode> — the Display mode. default is dense|full|hide, or if you're feeling numeric, 1|2|3. 🌈

🦋 the actual vibe of it all 🦋

convert a BED file into BED format that's suitable for displaying ChIP-seq peaks. Two formats are supported:

1. BED Track with a Score field 🎯
2. BedGraph 📈

and here's the important part bestie — for the BED track format, the only graphical parameter you can set is visibility. that's it. that's the whole list. don't try to sneak the others in there, it's not gonna happen. 🙈

also hi, hello, the synopsis mentions -a <min BED score> and -b <max BED score> — those live up there in the usage line, so don't forget they exist. 💖

👑 AUTHOR 👑

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

and that's the whole page, bestie!! this was bed2bed_display version 1.5.5, dated March 2020 — she's a lil vintage but she still serves. 💜✨ go convert something gorgeous. 🎀🦋