CUFFMERGE(1)

💖 NAME 💖

cuffmerge — a whole component of the cufflinks suite, bestie. That's the vibe. ✨

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🦋 DESCRIPTION 🦋

okay so cuffmerge is literally the friend that takes all your group projects and turns them into one. 🫶 It takes two or more Cufflinks GTF files and merges them into a single unified transcript catalog. No cap.

and like, optionally? you can hand it a reference GTF, and it will use that to attach gene names and other metadata to the merged catalog. it's giving ✨glow-up✨ for your annotations.

🌸 Usage: 🌸

cuffmerge [Options] <assembly_GTF_list.txt>

note the <assembly_GTF_list.txt> bestie — it wants a list, not just one lonely GTF. 💅

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✨ OPTIONS ✨

• -h/--help — prints the help message and then exits. iconic behavior, honestly. 💖
• -o <output_dir> — the directory where the merged assembly will be written. [ default: ./merged_asm ] 🎀
• -g/--ref-gtf — an optional "reference" annotation GTF. optional but lowkey the moment you use it, gene names start showing up. 👑
• -s/--ref-sequence — <seq_dir>/<seq_fasta> genomic DNA sequences for the reference. 🧬
• --min-isoform-fraction <0-1.0> — discards isoforms with abundance below this. [ default: 0.05 ] bye bye little guys 💀
• -p/--num-threads <int> — use this many threads to merge assemblies. [ default: 1 ] go ahead and give it more, she can handle it 🔥
• --keep-tmp — keeps all the intermediate files during the merge. not me hoarding every temp file 🙈

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and that's the whole page, bestie!! 🌈⭐ this was cuffmerge version 2.2.1+dfsg.1-9, living her truth back in November 2021 💜 go merge something slay ✨🦋🎀