STRINGTIE(1)

🌸 STRINGTIE(1) — User Commands 🌸

okay bestie, sit down, hydrate, because we're about to talk about stringtie and it's honestly iconic 💅 (this is the STRINGTIE(1) page, and yes it goes in section 1 of the manual, love that for us)

✨ NAME ✨

stringtie — assemble short RNAseq reads to transcripts 🧬🦋

💖 DESCRIPTION 💖

StringTie v2.1.6 usage:

stringtie <in.bam ..> [-G <guide_gff>] [-l <prefix>] [-o <out.gtf>] [-p <cpus>]
          [-v] [-a <min_anchor_len>] [-m <min_len>] [-j <min_anchor_cov>]
          [-f <min_iso>] [-c <min_bundle_cov>] [-g <bdist>] [-u] [-L] [-e]
          [--viral] [-E <err_margin>] [--ptf <f_tab>] [-x <seqid,..>]
          [-A <gene_abund.out>] [-h] {-B|-b <dir_path>} [--mix]
          [--conservative] [--rf] [--fr]

So the whole point, the moment, the vibe: this thing assembles RNA-Seq alignments into potential transcripts. That's it, that's the job. And here's every single knob it comes with 👇

• --version — just prints the version to stdout and dips out immediately. short and sweet, queen behavior 👑
• --conservative — conservative transcript assembly, same as -t -c 1.5 -f 0.05
• --mix — you're handing it both short AND long read data alignments
• --rf — assume stranded library fr-firststrand
• --fr — assume stranded library fr-secondstrand
• -G — reference annotation to use for guiding the assembly process (GTF/GFF3)
• --ptf — load point-features from a given 4 column feature file <f_tab>
• -o — output path/file name for the assembled transcripts GTF (default: stdout)
• -l — name prefix for output transcripts (default: STRG)
• -f — minimum isoform fraction (default: 0.01)
• -L — long reads processing; also enforces -s 1.5 -g 0 (default:false)
• -R — if long reads are provided, just clean and collapse the reads but do not assemble
• -m — minimum assembled transcript length (default: 200)
• -a — minimum anchor length for junctions (default: 10)
• -j — minimum junction coverage (default: 1)
• -t — disable trimming of predicted transcripts based on coverage (default: coverage trimming is enabled)
• -c — minimum reads per bp coverage to consider for multi-exon transcript (default: 1)
• -s — minimum reads per bp coverage to consider for single-exon transcript (default: 4.75)
• -v — verbose (log bundle processing details)
• -g — maximum gap allowed between read mappings (default: 50)
• -M — fraction of bundle allowed to be covered by multi-hit reads (default:1)
• -p — number of threads (CPUs) to use (default: 1)
• -A — gene abundance estimation output file
• -E — define window around possibly erroneous splice sites from long reads to look out for correct splice sites (default: 25)
• -B — enable output of Ballgown table files which will be created in the same directory as the output GTF (requires -G, -o recommended)
• -b — enable output of Ballgown table files but these files will be created under the directory path given as <dir_path>
• -e — only estimate the abundance of given reference transcripts (requires -G)
• --viral — only relevant for long reads from viral data where splice sites do not follow consensus (default:false)
• -x — do not assemble any transcripts on the given reference sequence(s)
• -u — no multi-mapping correction (default: correction enabled)
• -h — print this usage message and exit

🎀 Transcript merge usage mode 🎀

stringtie --merge [Options] { gtf_list | strg1.gtf ...}

With this option StringTie will assemble transcripts from multiple input files generating a unified non-redundant set of isoforms. In this mode the following options are available:

• -G <guide_gff> — reference annotation to include in the merging (GTF/GFF3)
• -o <out_gtf> — output file name for the merged transcripts GTF (default: stdout)
• -m <min_len> — minimum input transcript length to include in the merge (default: 50)
• -c <min_cov> — minimum input transcript coverage to include in the merge (default: 0)
• -F <min_fpkm> — minimum input transcript FPKM to include in the merge (default: 1.0)
• -T <min_tpm> — minimum input transcript TPM to include in the merge (default: 1.0)
• -f <min_iso> — minimum isoform fraction (default: 0.01)
• -g <gap_len> — gap between transcripts to merge together (default: 250)
• -i — keep merged transcripts with retained introns; by default these are not kept unless there is strong evidence for them
• -l <label> — name prefix for output transcripts (default: MSTRG)

😭 bestie. Error: no input file provided! — yeah, she will absolutely say that if you give her nothing to work with. feed the machine, pls 🙈

🌈 AUTHOR 🌈

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.

and that's the whole page, no cap 🫶 stringtie 2.1.6+ds, dated June 2021 — that's the source and the date, and honestly? periodt. go assemble something iconic 💜✨🍓