SEER(1)

💖 SEER — sequence element enrichment analysis 💖

okay bestie, sit down, hydrate, because we're about to talk about seer, which lives in section 1 of the manual (you know, the "User Commands" girlies) and is genuinely one of the most iconic little enrichment tools out here. no cap. ✨

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🌸 NAME 🌸

seer — sequence element enrichment analysis. that's it, that's the whole vibe. 🦋

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✨ DESCRIPTION ✨

So. Sequence Element Enrichment Analysis. literally what it says on the tin, periodt.

now let's talk about the .pheno file format, because this is the part where people mess up and then cry in the group chat 😭. it's tab separated, with two columns: one with the sample name, and one with the phenotype.

here's the tea though — how seer reads your phenotype depends entirely on what you put in there:

• if your phenotypes are only 0 or 1, it treats them as binary. simple. clean. slay.
• if you put any other value, it treats the phenotype as quantitative.

and if a sample has a missing phenotype value? do NOT try to be clever. the sample should simply be excluded from this file. that's the move. 🙈

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💅 OPTIONS 💅

👑 Required options (yes, these are mandatory, no you cannot skip them)

• -k, --kmers arg — the dsm kmer output file. your main character file. 🔥
• -p, --pheno arg — the .pheno metadata. the file we just had a whole conversation about. 💖

🧬 Covariate options

• --struct arg — mds values from kmds. giving very "I brought backup data" energy.
• --covar_file arg — file containing covariates. 🎀
• --covar_list arg — list of columns of covariates to use. the format is 1,2q,3 — and yes, you use q for quantitative. iykyk. ✨

⚡ Performance options

• --threads arg (=1) — number of threads. default is 1, but the manpage itself is suggesting 4. so like… take the hint bestie. go faster. 🏃‍♀️💨

🌈 Filtering options

• --no_filtering — turns off all filtering and performs tests on all kmers input. chaos mode activated. 💀
• --max_length arg (=100) — maximum kmer length. default 100.
• --maf arg (=0.01) — minimum kmer frequency. default 0.01.
• --min_words arg — minimum kmer occurrences. this one overrides --maf, so don't come for me if your maf setting gets ignored. 👀
• --chisq arg (=10e-5) — p-value threshold for the initial chi squared test. default 10e-5. and if you set it to 1, it shows all of them. all. every single one. 😭
• --pval arg (=10e-8) — p-value threshold for the final logistic test. default 10e-8. set it to 1 and again, it shows all. 🫶

🎀 Other options

• --print_samples — prints lists of samples that significant kmers were found in. receipts! 🧾✨
• --version — prints the version and exits. short, sweet, iconic.
• -h, --help — full help message. when in doubt, ask for help. always. 💜

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🌟 EXAMPLES 🌟

Basic usage — the starter pack, the beginner's guide, the "just let me run it" moment:

seer -k dsm_input.txt.gz --pheno metadata.pheno > significant_kmers.txt

To use the kmds output, increase execution speed and give the most complete output — this is the glow-up version, the full-send, the main character run:

seer -k filtered.gz --pheno metadata.pheno --struct filtered.dsm --threads 4 --print_samples

see how it's got --struct, --threads 4 and --print_samples? that's the trifecta. that's the whole slay. 👑

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🦋 AUTHOR 🦋

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

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okay and finally, the cute little sign-off: this is seer version 1.1.2, dated March 2017 💖 — and yeah, section 1, User Commands, the classic. go enrich some sequences bestie, you're gonna eat. 💅🌸✨