BAM2HINTS(1)

📦
version 3.5.0 · 5 versions
, in ubuntu resolute, ubuntu stonking

✨ BAM2HINTS(1) ✨

okay bestie, welcome to bam2hints, section 1 of the manual, and she is so iconic 💖

🌸 NAME 🌸

bam2hints — the glow-up machine that converts mRNA-to-genome alignments in BAM format into a hint file for AUGUSTUS. that's it, that's the girl 🎀

🦋 SYNOPSIS 🦋

bam2hints [parameters] [--in=example.bam] [--out=hints.gff]

💅 OPTIONS 💅

okay so before we even get to the flags, there's a vibe check you literally cannot skip:

The input BAM file must be sorted by target (= genome) sequence names, and within those sequences by begin coordinates. no cap. if it's not sorted like that, we're not doing this. 🙈

🍓 Parameters:

  • --in=example.bam — the input BAM file, your main character. you can only skip this one on UNIX platforms — and when you do, bam2hints reads from the standard input stream instead. slay 💫
  • --out=hints.gff — the output hints gff file. if you don't pass this, bam2hints writes to the standard output stream. (yes bestie, stdout is always there for you 🫶)
  • --priority=n/-p — priority of hint group (set to 4) 👑
  • --maxgaplen=n/-g — gaps at most this length are simply closed, like no drama (set to 14) ✨
  • --minintronlen=n/-m — alignments with gaps shorter than this and longer than maxgaplen are discarded (set to 32). middle-ground queen 💀
  • --maxintronlen=n/-M — alignments with longer gaps are discarded, bye (set to 350000)
  • --MinEndBlockLen=n/-b — minimum length of a 'dangling' exon (set to 8) 🦋
  • --maxQgaplen=n/-q — maximum length of gap in the query (cDNA) sequence (set to 5)
  • --exonhints/-x — compute exonpart, exon and splice site hints in addition to intron hints (set to 0 = Off). ok and here's the tea: you should generate exonpart hints from RNA-Seq using wiggle (.wig) input to wig2hints instead. iykyk 🌈
  • --ep_cutoff=n/-e — this many bp are cut off of each exonpart hint at the end of the alignment (set to 10) ✂️
  • --source=s/-s — source identifier (set to 'E') 🏷️
  • --intronsonly/-I — only retrieve intron hints (like, for example, because the exon(part) hints are retrieved by converting to a wig track; set to 1 = On). Deprecated — because this is literally the default now, bestie. it's giving legacy 💀
  • --nomult/-n — do not summarize multiple identical intron hints to a single one (set to 0 = Off) 🙅
  • --remove_redundant/-r — only keep the strongest hint for a region (set to 0 = Off). survival of the fittest 🏆
  • --maxcoverage=n/-C — maximal number of hints at a given position (0 = filtering deactivated). careful though — a high value causes long running time of AUGUSTUS in regions with thousands of cDNA alignments. she will be slow 😭 (set to 0)
  • --ssOn/-S — include splice site (dss, ass) hints in output (set to 0 = Off) ✂️✨
  • --trunkSS/-T — include splice site hints from the ends of a truncated alignment (contig too short, set to 0 = Off) 🫠
  • --score=f/-s — fill this number in in the score column (set to 0) 🔢
  • --maxgenelen=n/-G — alignments of the same clone are considered to be of the same gene if not separated by more than this (set to 400000). alignments that span more than this are ignored, but lowkey just filter long introns through an alignment program instead, fr fr 🧚

👑 AUTHORS 👑

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. absolute legends, periodt 💜

📚 ADDITIONAL DOCUMENTATION 📚

an exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz. go read it, it eats 💖

and that's the whole BAM2HINTS(1) manual page, section 1, bestie — no date on this one, just pure bam2hints(1) energy from the AUGUSTUS docs. mwah, go make some hints 🎀✨💅

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