CREATE_DROP-...E_METADATA.SH(1)

✨ NAME ✨

create_Drop-seq_reference_metadata.sh — the girlies that spins you up a whole Drop-seq reference metadata bundle 💅

Like, this is a User Commands situation, bestie. Manual page energy, lowercase filename, big responsibilities. 🎀

🦋 DESCRIPTION 🦋

okay so here's the vibe check on how you actually call her:

USAGE: create_Drop-seq_reference_metadata.sh [options]

That's it. That's the whole entrance. She takes options, she makes you a reference metadata bundle, she slays. 🌸

🌈 OPTIONS 🌈

• -n <name> — the Name for the reference metadata set you're about to create. Required. No name, no bundle, no cap. 💀
• -r <referencefasta> — the Reference fasta of the Drop-seq reference metadata bundle. Required. She literally cannot do it without this one bestie. 🧚
• -s <species> — the Species. Required. Yes she needs to know. 🦋
• -g <gtf> — the Gene annotation file. Required. Fourth required one, we stay consistent. ✨
• -f <filtered-gene-biotype> — any annotations carrying the given gene_biotype get filtered out. You can flex multiple values by throwing this argument more than once, and/or by handing her a comma-separated list. And listen — run the ValidateReference command first so you can actually see the gene_biotypes chillin' in your GTF, and then decide what to exclude. Default: not gene biotypes are filtered. (i.e. out of the box, nothing gets filtered. 🫶)
• -d <dropseq_root> — the Directory containing Drop-seq executables. Default: the directory containing this script. She knows where she lives. 👑
• -o <outputdir> — Where to write output bam. Default: current directory. 🍓
• -t <tmpdir> — Where to write temporary files. Default: Value of 132153TMPDIR environment variable. (that's literally what it says, i am not editing the queen's typo 😭)
• -a <STAR_path> — Full path of STAR. Default: STAR is found via PATH environment variable. 🌟
• -b <bgzip_path> — Full path of bgzip: Default: bgzip is found via PATH environment variable.
• -i <samtools_path> — Full path of samtools. Default: samtools is found via PATH environment variable.
• -v — verbose 👀 (she tells you everything)
• -e — merely echo commands instead of executing. so like, she says the thing but doesn't do the thing. main character of a dress rehearsal. 💅

🔥 SEE ALSO 🔥

Drop-seq_alignment.sh(1) — go read that one too, iykyk 🌈

💖 okay that's the whole page bestie, go make that metadata bundle. periodt. 💖

signing off from create_Drop-seq_reference_met..., dated February 2021, source/version stamp CREATE_DROP-...E_METADATA.SH(1) — xoxo, your favorite manual page 💜