COUNTSGA(1)

🎀 NAME 🎀

countsga — okay so bestie, this little icon reads a ChIP-seq data file and computes the total number of tag counts. That's the whole job. She's simple, she's effective, she ate. 💅

✨ SYNOPSIS ✨

countsga [options] [<] <SGA File>

🌸 DESCRIPTION 🌸

This is version 1.5.5 bestie, and the options are literally right here:

• -h — shows you this help text, like a little hand-holding moment 🫶
• -d — prints debug information, so when something's weird you can actually see what's going on 👀
• -f — feature specifications, formatted as name [+|-]
• -c — the Count Cut-off, and the default is 1 (not me forgetting the default, couldn't be me)

So here's the vibe: the program reads a ChIP-seq data file (or it reads from stdin if you hit it with [<]) in SGA format, aka your <SGA File>, and then it computes the total number of tag counts and the total sequence length. Two things. At once. Multitasking queen 👑

The <Feature> parameter is a name that corresponds to the second field of the SGA file. It might optionally include the strand specification, which is + or -. And if you don't give it a feature at all? Then all input tags get processed. No feature, no problem. Periodt. 💖

ngl bestie, if you're passing a <Feature>, double check it matches the second field of your SGA file, because that's literally the field it's reading. iykyk.

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. We love a generous king 🫶✨

And that's a wrap on countsga version 1.5.5, dated March 2020, filed under COUNTSGA(1) in the User Commands section of the manual. Slay, read responsibly, and go count some tags bestie 🌈💜