UMIS(1)

📦 version 1.0.9, in debian bookworm, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ UMIS ✨

okay bestie, gather round, because this is the umis manual page and it's literally your new best friend for UMI RNA-tag data 💖

🌸 NAME 🌸

umis — tools for processing UMI RNA-tag data

like. that's the whole vibe. tools. for UMI RNA-tag data. slay. 🧬✨

🎀 SYNOPSIS 🎀

umis [OPTIONS] COMMAND [ARGS]...

so you run umis, you can hand it some [OPTIONS], then you pick a COMMAND, and then that command gets its own [ARGS]... 🫶

💅 OPTIONS 💅

  • --help — shows you this message and then dips. that's it. that's the option. iconic behaviour honestly 👑

🦋 Commands 🦋

here's the whole squad, no gatekeeping:

  • add_uid — Adds UID:[samplebc cellbc umi] to readname for...
  • bamtag — Convert a BAM/SAM with fastqtransformed read names to...
  • cb_filter — Filters reads with non-matching barcodes Expects...
  • cb_histogram — Counts the number of reads for each cellular barcode...
  • demultiplex_cells — Demultiplex a fastqtransformed FASTQ file into a...
  • demultiplex_samples — Demultiplex a fastqtransformed FASTQ file into a...
  • fastqtransform — Transform input reads to the tagcounts compatible...
  • fasttagcount — Count up evidence for tagged molecules, this...
  • kallisto — Convert fastqtransformed file to output format...
  • mb_filter — Filters umis with non-ACGT bases Expects formatted...
  • sb_filter — Filters reads with non-matching sample barcodes...
  • sparse — Convert a CSV file to a sparse matrix with rows and...
  • subset_bamfile — Subset a SAM/BAM file, keeping only alignments from...
  • tagcount — Count up evidence for tagged molecules
  • umi_histogram — Counts the number of reads for each UMI Expects...
  • version
ngl bestie, a bunch of these descriptions trail off mid-sentence in the original and I am not about to invent the rest, so they stay exactly like that. run umis <command> --help and let the tool speak for itself 💀

👑 AUTHOR 👑

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

periodt. he ate that. 🎀

okay so final sign-off bestie: this is umis 1.0.3, dated April 2019, and yes we're still calling it UMIS(1) 💖✨ go process some UMI RNA-tag data, you main character 🦋

📦 where this page comes from