SGA2WIG(1)

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

🎀 NAME 🎀

okay so this is the SGA2WIG(1) page bestie, and the whole entire point of it is this: sga2wig — convert SGA format into Wiggle Track format. that's it. that's the girl. 💖

🌸 SYNOPSIS 🌸

sga2wig [options] [<] <SGA file|stdin>

so you either hand her a file, or you pipe stuff in with < and stdin. she's flexible like that. 💅

✨ DESCRIPTION ✨

this is version 1.5.5, and here are the options, all of them, no skips, we don't do skips in this house 🫶

💅 the options 💅

  • -d|--debug — produce Debug information. for when you wanna see the receipts 🔍
  • -h|--help — show this Help text. hi bestie 👋
  • -i|--db <path> — use <path> to locate the chr_NC_gi and chr_size files [default is: $HOME/db/genome]
  • -o|--format <0|1> — set the Wiggle Track data format: variableStep [def=0] or fixedStep [1]
  • -n|--chrnb — <int> chromosome number [def: 0 (all chromosomes)]. zero means she does every single chromosome, main character behavior
  • -b|--start — <int> chromosome start [def: -1 (entire chromosome)]
  • -e|--end — <int> chromosome end [def: -1 (entire chromosome)]
  • -c|--coff — <int> count cut-off for the SGA input file [def=99999]
  • -s|--span — <int> Wiggle Track Span(/stepInterval) parameter [def=150]
    • for fixedStep data format, it defines the step parameter
  • -f|--norm — <int> normalization factor for total tag counts within step intervals [def=0]
    • > heads up babes: this option is only valid for fixedStep data format
  • --peakf — indicate that the The SGA input file represents a peak file [i.e. coordinates are peak centers]. in such case, the span range begins upstream of [span=]150 bp chromosome position specified, and ends [span=]150 bp downstream
  • --name <name> — set name for track name field [def. name=SGA-feature]
  • --desc <desc> — set track description field [def. desc="ChIP-Seq Custom data"]
  • --color <col> — define the track color in comma-separated RGB values [def. 100,100,100]
  • --autoscale — <on|off> data viewing paramenter: set auto-scale to UCSC data view [def=OFF]
  • --always0 — <on|off> data viewing paramenter: always include zero [def=OFF]
  • --wfunction — <func> data viewing paramenter: windowing function [def=mean+whiskers|maximum|mean|minimum]
  • --smoothing — <grade> data viewing paramenter: smoothing window [def=OFF[0], <grade>=0,2..16]
  • --visibility <mode> — display mode: [def=full|dense|hide]

🦋 the actual conversion tea 🦋

convert SGA format into Wiggle Track format (WIG). WIG format is line-oriented, and is composed of declaration lines and data lines. simple as that ✨

  • variableStep is for data with irregular intervals between new data points.

it begins with a declaration line and is followed by two columns containing chromosome positions and data values:

variableStep chrom=chrN  [span=windowSize]

chromStartA  dataValueA
chromStartB  dataValueB
... etc ...
  • fixedStep is for data with regular intervals between new data values.

it begins with a declaration line and is followed by a single column of data values:

fixedStep chrom=chrN  start=position  step=stepInterval  [span=windowSize = stepInterval]

dataValue1 dataValue2 ... etc ...

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. king behavior, we stan 🫡💜

that's the whole page bestie, no cap. this was sga2wig 1.5.5, dated March 2020, and you absolutely ate for reading all the way down here. periodt. 🎀✨🦋💅

📦 where this page comes from