EXPRESS(1)

💖 EXPRESS(1) 💖

okay bestie, welcome to EXPRESS(1) — that's the manual page name, don't @ me — aka berkeley-express, the streaming quantification icon for high-throughput sequencing. she's a User Command, she's lowkey legendary, and she's about to make your RNA-seq life so much easier. let's get into it 🧚✨

🌸 NAME 🌸

berkeley-express — Streaming quantification for high-throughput sequencing 💅

🦋 DESCRIPTION 🦋

so the way that eXpress works is, you can either hand her files directly or pipe stuff straight into her. both are valid, both are iconic. pick your fighter:

File Usage:

express [options] <target_seqs.fa> <hits.(sam/bam)>

Piped Usage:

bowtie [options] -S <index> <reads.fq> | express [options] <target_seqs.fa>

fr fr, she reads from stdin if you pipe it, no cap 🫶

🎀 Required arguments:

like, these ones are not optional, bestie. she needs them. periodt.

• <target_seqs.fa> — target sequence file in fasta format 🌱
• <hits.(sam/bam)> — read alignment file in SAM or BAM format 📎

⭐ Standard Options:

• -h, --help — produce help message. she's helpful like that 💁‍♀️
• -o, --output-dir arg (=.) — write all output files to this directory 📁 default is literally just .
• -D, --preprocess — run preprocess script for eXpressD ✨
• -m, --frag-len-mean arg (=200) — prior estimate for average fragment length 📏
• -s, --frag-len-stddev arg (=80) — prior estimate for fragment length std deviation 📐
• -H, --haplotype-file arg — path to a file containing haplotype pairs 👯
• -B, --additional-batch arg (=0) — number of additional batch EM rounds after initial online round 🔁
• -O, --additional-online arg (=0) — number of additional online EM rounds after initial online round 🔂
• -L, --max-read-len arg (=250) — maximum allowed length of a read 📖
• --output-align-prob — output alignments (sam/bam) with probabilistic assignments 🎲
• --output-align-samp — output alignments (sam/bam) with sampled assignments 🎯
• --fr-stranded — accept only forward->reverse alignments (second-stranded protocols) ➡️⬅️
• --rf-stranded — accept only reverse->forward alignments (first-stranded protocols) ⬅️➡️
• --f-stranded — accept only forward single-end alignments (second-stranded protocols) ➡️
• --r-stranded — accept only reverse single-end alignments (first-stranded protocols) ⬅️
• --no-update-check — disables automatic check for update via web 🙈
• --logtostderr — prints all logging messages to stderr 📢

👑 Advanced Options:

this is where the main character energy lives. buckle up 🍓

• -f, --forget-param arg (=0.84999999999999998) — sets the 'forgetting factor' parameter (0.5 < c <= 1) 💭
• --library-size arg — specifies library size for FPKM instead of calculating from alignments 📊
• --max-indel-size arg (=10) — sets the maximum allowed indel size, affecting geometric indel prior 🧬
• --calc-covar — calculate and output covariance matrix 🔢
• --expr-alpha arg (=0.0050000000000000001) — sets the strength of the prior, per bp ⚖️
• --stop-at arg (=0) — sets the number of fragments to process, disabled with 0 🛑
• --burn-out arg (=5000000) — sets number of fragments after which to stop updating auxiliary parameters 🔥
• --no-bias-correct — disables bias correction 🚫
• --no-error-model — disables error modelling 🚫
• --aux-param-file arg — path to file containing auxiliary parameters to use instead of learning 📂

💖 reminder bestie: every option here is exactly as written — no renaming, no merging, no inventing. copy them character for character or she will Not be happy with you. 🙈

and that's the whole vibe check, bestie 🌈 go quantify something gorgeous. this page is for express version 1.5.1, dated February 2015 — yeah she's vintage but she ATE, and honestly? still slay. 💅✨🦋👑