TRINITY(1)

✨ Trinity: User Commands ✨

Hiii bestie, we're in Trinity territory today, filed under User Commands 💖🦋

🌸 NAME 🌸

Trinity — RNA-Seq De novo Assembly 🧚

🔥 DESCRIPTION 🔥

okay so Trinity is a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. it's giving main character energy 💅 It combines three independent software modules, Inchworm, Chrysalis, and Butterfly, and runs them one after another to chew through huge piles of RNA-seq reads ✨

here's the iconic part 👑 Trinity splits the sequence data into lots of individual de Bruijn graphs. each graph represents the transcriptional complexity at one gene or locus. then it processes every graph on its own to pull out full-length splicing isoforms and to untangle transcripts that come from paralogous genes. literally so smart 😭

💖 OPTIONS 💖

Required

• --seqType <string> — the type of reads you're feeding it: fa or fq 🍓
• --max_memory <string> — the suggested max memory Trinity can use, in places where it can be limited (jellyfish, sorting, etc). give it in Gb of RAM, ie. '--max_memory 10G' 🧠

If paired reads

• --left <string> — left reads, one or more (separated by space) 👈
• --right <string> — right reads, one or more (separated by space) 👉

Or, if unpaired reads

• --single <string> — single reads, one or more. ngl if your single file actually contains pairs, you can use the flag --run_as_paired instead 🦋

Misc

• --SS_lib_type <string> — strand-specific RNA-Seq read orientation. if your reads are paired it's RF or FR, and if they're single it's F or R. (the dUTP method is RF) check the web documentation for the tea 🫶
• --CPU <int> — how many CPUs to use. default is 2 💅
• --min_contig_length <int> — the minimum assembled contig length to report. default is 200 (def=200) ✨
• --long_reads <string> — a fasta file with error-corrected or circular consensus (CCS) PacBio reads 🌈
• --genome_guided_bam <string> — genome guided mode! give it the path to a coordinate-sorted bam file. see the genome-guided param section under --show_full_usage_info for the deets 🗺️
• --jaccard_clip — an option you set if you have paired reads and you expect high gene density with UTR overlap (use FASTQ input for your reads).

bestie, warning 💀 --jaccard_clip is an expensive operation, so only use it when you actually need it. you'd only reach for it if you're finding excessive fusion transcripts without it.

• --trimmomatic — runs Trimmomatic to quality trim your reads. check --quality_trimming_params under full usage info for tailored settings 🧼
• --normalize_reads — runs in silico normalization of reads. it defaults to a max read coverage of 50. see --normalize_max_read_cov under full usage info for tailored settings ⚖️
• --no_distributed_trinity_exec — skips Trinity phase 2 (assembly of partitioned reads) and stops after generating the command list 🛑
• --output <string> — the name of the directory for output. it'll get created if it doesn't already exist. default is your current working directory 📁
• --full_cleanup — only keeps the Trinity fasta file, renamed as ${output_dir}.Trinity.fasta 🧹
• --cite — shows the Trinity literature citation 📚
• --version — reports the Trinity version (Trinity_v2.0.2) and then exits 🔖
• --show_full_usage_info — shows the many many more options for running Trinity. expert mode only 🧙‍♀️

🎀 EXAMPLES 🎀

okay so a typical Trinity command might look like this 🍓

Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6

and for Genome-guided Trinity, it's giving this 🌸

Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G --genome_guided_max_intron 10000 --CPU 6

🦋 SEE ALSO 🦋

see /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/ for sample data, and runMe.sh for example Trinity execution 🧚

for more details, visit http://trinityrnaseq.github.io 💜

okay bestie that's the whole tea ☕💖 this page was Trinity Trinity_v2.0.2, last updated February 2015, filed under TRINITY(1) 🫶✨