CONV_GTF_TO_BED(1)

💖 CONV_GTF_TO_BED 💖

okay bestie, welcome to the manual page for conv_gtf_to_bed — that's section 1 of the manual, the User Commands zone, the place where executables live. pull up a chair, grab a strawberry 🍓, we're doing this.

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✨ NAME ✨

conv_gtf_to_bed — the legacy script that calls the PALEOMIX command gtf_to_bed. it's giving "old faithful", it's giving "the vibes are historic but the job still gets done". 🫶

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🌈 SYNOPSIS 🌈

paleomix gtf_to_bed [options] in.gtf out_prefix [in.scaffolds]

that's it, that's the whole shape of it. options first, then your input, then your prefix, and maybe a scaffolds file if you're feeling spicy. 💅

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🦋 DESCRIPTION 🦋

so. the PALEOMIX pipelines are a whole little ecosystem of pipelines and tools, and their whole mission is helping you process High-Throughput Sequencing (HTS) data at speed. rapid processing, no waiting around, periodt. here's the lineup:

• the BAM pipeline takes de-multiplexed reads from one or more samples and runs them all the way through sequence processing and alignment, spitting out BAM alignment files that are useful for whatever downstream analyses you've got cooking.
• the Phylogenetic pipeline does genotyping and phylogenetic inference on BAM alignment files — doesn't matter if those files came from the BAM pipeline or were generated somewhere else entirely, she's not picky.
• the Zonkey pipeline runs a whole suite of analyses on low coverage equine alignments, specifically to detect whether F1-hybrids are hanging out in archaeological assemblages. yes, zonkey. iconic name. no notes. 🦓

and on top of all that, PALEOMIX also helps with metagenomic analysis of the extracts. multitasking queen 👑

the pipelines were designed with ancient DNA (aDNA) in mind, and they include several features that are especially useful for analysing ancient samples — but lowkey they can all be used for processing modern samples too, because the goal is consistent data processing across the board. same treatment, same energy, every sample. ✨

now, conv_gtf_to_bed specifically? it's a legacy script for invoking the paleomix(1) command gtf_to_bed. that's the whole job description. she's a little bridge, and she's thriving. 🌉

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🎀 OPTIONS 🎀

🌸 positional arguments:

• INPUT.gtf — your input file, and it's gotta be in GTF format. no GTF, no party.
• OUTPUT_PREFIX — the prefix that all your output files will get. the little name-tag situation. 🏷️
• SCAFFOLDS — a mapping of scaffolds to contig positions; for example, mapping individual Un* scaffolds onto chrUn. the "where does this actually belong" file.

💜 optional arguments:

• -h, --help — shows this help message and then exits. the classic. the moment you need it most, she's there. 🙈
• --keep-all-transcripts — include all transcripts in the output BED files, not just the longest transcript of each gene. [default: off]
• --keep-malformed-proteins — include transcripts of protein-coding in the output even if the length of the CDS is not divisible by 3. yes, even the messy ones. [default: off]
• --contig-prefix CONTIG_PREFIX — add a prefix to contig names (e.g. 'chr'). [default: no prefix].

heads up bestie: all three of those long options default to off / no prefix, so if you want them, you gotta ask for them out loud. the default is the default for a reason. 💀

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👑 SEE ALSO 👑

paleomix(1)

go read that one too, she's the main character here. 💖

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🧚 AUTHOR 🧚

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. thank you Andreas, we appreciate you, genuinely. 🫶🌸

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and that's the whole page, bestie!! conv_gtf_to_bed version 1.2.7, dated February 2017 — a little vintage, a little legendary, and honestly? she ate. 💅✨🎀