LAST-PAIR-PROBS(1)

💖 LAST-PAIR-PROBS 💖

okay so bestie, welcome to last-pair-probs from the User Commands corner of the manual — it's giving "genomics girlie with a calculator" and honestly? iconic. 🧬✨

🌸 NAME 🌸

last-pair-probs — read alignments of paired DNA reads to a genome, and do estimations. that's it, that's the whole vibe. 🫶

✨ SYNOPSIS ✨

last-pair-probs [options] interleaved-alignments

last-pair-probs [options] alignments1 alignments2

two ways in, bestie — either one interleaved file or two separate ones. pick your fighter. 💅

🦋 DESCRIPTION 🦋

so like, you feed it alignments of paired DNA reads against a genome, and it does two whole things for you:

1. estimates the distribution of distances between paired reads 📏
2. estimates the probability that each alignment represents the genomic source of the read 🎯

no cap, that's the entire job description. it ate. 👑

🎀 OPTIONS 🎀

• -h, --help — show this help message and exit. the classic. the icon. 🫶
• -r, --rna — assume the reads are from potentially-spliced RNA. spliced girlies rise 🧬✂️
• -e, --estdist — just estimate the distribution of distances. nothing else, just the distances, we're being minimal 💅
• -m M, --mismap=M — don't write alignments with mismap probability > M. default is 0.01 🚫
• -f BP, --fraglen=BP — mean distance in bp 📐
• -s BP, --sdev=BP — standard deviation of distance 📊
• -d PROB, --disjoint=PROB — prior probability of disjoint mapping. default is 0.02 if you passed -r, otherwise 0.01 🎲
• -c CHROM, --circular=CHROM — specifies that chromosome CHROM is circular. default is chrM 🔄
• -V, --version — show program's version number and exit 👋

ngl bestie, don't sleep on the defaults — 0.01 vs 0.02 for -d literally flips based on whether you said -r, and chrM is just assumed circular unless you tell it otherwise. iykyk. 🙈

last-pair-probs 712 · December 2015 — yeah she's an elder but she's still serving, and this little manual page came straight from the User Commands section. periodt. 💖✨🎀