FLATTENGTF(1)

🌸 FLATTENGTF 🌸

okay bestie, come sit with me, we're gonna talk about flattenGTF — it's a whole toolkit for processing next-gen sequencing data, and honestly? it eats. 💅

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✨ NAME ✨

flattenGTF — toolkit for processing next-gen sequencing data 🧬

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💖 DESCRIPTION 💖

flattenGTF Version 2.0.4

So what does it actually do? It flattens the features chillin' inside a GTF annotation, then saves that modified annotation out to a SAF format file. That's it. That's the whole vibe. ✨

🎀 Usage:

./flattenGTF [options] -a <input_file> -o <output_file>

🫶 Mandatory arguments:

these are NOT optional, bestie, you literally cannot skip them:

• -a <file> — the name of an annotation file in GTF/GFF format. like, the one you're feeding in. 🍓
• -o <file> — the name of the output file. where the magic lands. 💖

🌈 Optional arguments:

these ones you can skip, but why would you, they're iconic:

• -t <string> — specify the feature type in a GTF annotation. defaults to 'exon'. features with the feature type you name get extracted from the annotation and sent off for processing. lowkey the main character selector. 👑
• -g <string> — specify the attribute type in GTF annotation. defaults to 'gene_id'. this attribute type is what groups features together into metafeatures. fr fr, it's the grouping glue. 🧚
• -C — merges overlapping exons into multiple non-overlapping exons, but all the edges are kept. not me keeping every single edge, we love a thorough queen. 💅

heads up bestie: -t defaults to 'exon' and -g defaults to 'gene_id' — don't come for me if you forgot, the defaults got you. 🫶

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👑 AUTHOR 👑

This manpage was written by Alexandre Mestiashvili for the Debian distribution and can be used for any other usage of the program. giving credit where credit is due, periodt. 💜

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flattenGTF 2.0.3 · March 2023

and that's the whole page, bestie — slay, go flatten some features, i'm obsessed with you. 🦋✨💖