INSEGT(1)

✨ INSEGT(1) ✨

okay so bestie, this is the insegt manual page — short for INtersecting SEcond Generation sequencing daTa with annotation 🧬💖. She's a little command-line queen and honestly? iconic. Let's get into it.

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🌸 NAME 🌸

insegt — INtersecting SEcond Generation sequencing daTa with annotation

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🦋 SYNOPSIS 🦋

insegt [OPTIONS] <ALIGMENTS-FILE> <ANNOTATIONS-FILE>

(yes the flag spellings are exactly like that, no cap, we do not fix what we did not break 💅)

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👑 DESCRIPTION 👑

Okay so INSEGT is a tool for analyzing alignments of RNA-Seq reads — single-end or paired-end, she does both, versatile 💅 — by using gene-annotations.

The input to INSEGT is a SAM file containing the alignments, plus a file containing the annotations of the reference genome, either in GFF or GTF format. Two files in, science out. periodt. ✨

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🎀 REQUIRED ARGUMENTS 🎀

• ARGUMENT 0 INPUT_FILE — valid filetype is: .sam. 📄
• ARGUMENT 1 INPUT_FILE — valid filetypes are: .gtf and .gff. 📑✨

fr fr these two are not optional. she needs them. feed her or she will simply not run 💀

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💖 OPTIONS 💖

• -h, --help — displays the help message. when in doubt, ask her nicely 🫶
• --version — displays version information. she'll tell you who she is 💁‍♀️

✨ Options: : ✨

(that heading is genuinely what it says, i'm not even joking, leaving it exactly as-is 😭)

• -ro, --read-output OUTPUT_FILE — output filename for read-output, which contains the mapped annotations followed by their parent annotation. Valid filetype is: .gff. 🌈
• -ao, --anno-output OUTPUT_FILE — output filename for anno-output, which contains the annotations similar to the GFF input, plus the counts of the mapped reads and the normalized expression levels in RPKM. Valid filetype is: .gff. 📊
• -to, --tuple-output OUTPUT_FILE — output filename for tuple-output, which contains exon tuples connected by reads or matepairs. Valid filetype is: .gff. 🔗
• -fo, --fusion-output STRING — output filename for fusion-output, which contains exon tuple of gene fusions. This one is an Advanced option, and currently there's no output port for KNIME. One of gff. 🧪
• -n, --ntuple INTEGER — ntuple. Default: 2. 🔢
• -o, --offset-interval INTEGER — offset to short alignment-intervals for search. Default: 5. 📐
• -t, --threshold-gaps INTEGER — threshold for allowed gaps in alignment (not introns). Default: 5. 🚧
• -c, --threshold-count INTEGER — threshold for min. count of tuple for output. Default: 1. 🔢
• -r, --threshold-rpkm DOUBLE — threshold for min. RPKM of tuple for output. Default: 0.0. 📈
• -m, --max-tuple — create only maxTuple (which are spanned by the whole read). 🏆
• -e, --exact-ntuple — create only Tuple of exact length n. By default all tuple up to the given length are computed — but heads up: if -m is set, -e will be ignored. ⚠️
• -u, --unknown-orientation — orientation of reads is unknown. 🤷‍♀️

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🌟 EXAMPLES 🌟

okay here are the little demo runs, all living in the example/ folder 🍓

1. Run INSEGT on example files with default parameters:

insegt  example/alignments.sam example/annotations.gff

1. Run INSEGT on example files and only compute maxTuple:

insegt -m example/alignments.sam example/annotations.gff

1. Run INSEGT on example files and only output tuple with a min. count of 2:

insegt -c 2 example/alignments.sam example/annotations.gff

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💜 and that's the whole page bestie. go align something. iykyk.

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that's a wrap on the insegt manual — this is insegt 1.1.14, shipped as a [tarball], and i'd like to thank her for her service 🫡💖 stay hydrated, read your SAM files, and may your tuples always be connected. bye bestie!! ✨🎀🦋🌸