DROP-SEQ_ALIGNMENT.SH(1)

✨ NAME ✨

okay bestie, meet Drop-seq_alignment.sh, the script that does Drop-seq tagging, trimming and alignment all in one go 💖 it's literally a whole pipeline in a trench coat 🧥

🌸 DESCRIPTION 🌸

So the way you call it is:

USAGE: Drop-seq_alignment.sh [options] <unmapped-queryname-sorted.bam>

Give it an unmapped, queryname-sorted BAM and it handles the rest. The [options] are where the main character energy lives 👑

🎀 OPTIONS 🎀

• -g <genomedir> — Point it at your STAR genome directory. This one is required, no skipping 🙅‍♀️
• -r <referencefasta> — The reference fasta from your Drop-seq reference metadata bundle. Also required, don't forget it 💀
• -d <dropseq_root> — Where the Drop-seq executables live. If you don't set it, it defaults to the directory that holds this script 🧚
• -o <outputdir> — Where the output bam gets written. Default is the current directory 🍓
• -t <tmpdir> — Where the temp files go. Default is a brand new subdirectory in . 🦋
• -s <STAR_path> — The full path to STAR. If you leave it out, it hunts STAR down through the PATH environment variable 🔍
• -e — Echo the commands instead of actually running them. Good for a vibe check before anything runs 👀
• -k — Keep the intermediate files so they don't get deleted 🫶

🔗 SEE ALSO 🔗

bestie, check out create_Drop-seq_reference_metadata.sh(1) too, it's the perfect companion 💜

Okay that's the tea 🫖 This page was brought to you by Drop-seq_alignment.sh, source version from February 2021 🌈 slay forever 💅✨