CUFFCOMPARE(1)

💖 CUFFCOMPARE 💖

okay bestie, welcome to cuffcompare — she's a whole component of the cufflinks suite and she's lowkey the group-chat admin of your transcript data. ✨

this is cuffcompare v2.2.1 (Debian package), no cap. 👑

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🌸 SYNOPSIS 🌸

cuffcompare [-r <reference_mrna.gtf>] [-R] [-T] [-V] [-s <seq_path>]
            [-o <outprefix>] [-p <cprefix>] {-i <input_gtf_list> |
            <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}

like... she takes either a list file or a whole pile of GTF files straight up. pick your fighter. 💅

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🦋 DESCRIPTION 🦋

so cuffcompare provides classification, reference annotation mapping and a bunch of various statistics for Cufflinks transfrags. she's giving main character energy fr fr.

she clusters and tracks transfrags across multiple samples, and writes:

• the matching transcripts (aka intron chains) into <outprefix>.tracking 🎀
• a GTF file <outprefix>.combined.gtf with a nonredundant set of transcripts across all your input files (and for each clique of matching transfrags across samples, exactly one single representative transfrag gets chosen — queen behaviour, only one of y'all is speaking 💅)

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✨ OPTIONS ✨

• -i — give her a text file with a list of Cufflinks GTF files to process instead of expecting them as command line arguments. lowkey iconic when you've got a large number of GTF files and no desire to type them all out. 🫶
• -r — a set of known mRNAs to use as a reference for assessing the accuracy of the mRNAs or gene models given in <input.gtf>. your benchmark bestie. 📏
• -R — for the -r option: consider only the reference transcripts that overlap any of the input transfrags (this is the Sn correction). 🙈
• -Q — for the -r option: consider only the input transcripts that overlap any of the reference transcripts (this is the Sp correction).

⚠️ Warning: this will discard all "novel" loci! not a drill, bestie, the novel ones are GONE. 💀

• -M — discard (ignore) single-exon transfrags and reference transcripts. bye. 👋
• -N — discard (ignore) single-exon reference transcripts. (just the reference ones this time, she's being specific 🎀)
• -s <seq_path> — can be a multi-fasta file with all the genomic sequences, or a directory containing multiple single-fasta files (one file per contig). lower case bases will be used to classify input transcripts as repeats. 🌈
• -e — max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. default is 100. 🍓
• -d — max. distance (range) for grouping transcript start sites. default is 100. 💜
• -p — the name prefix to use for consensus transcripts in the <outprefix>.combined.gtf file. default is 'TCONS'. 👑
• -C — include the "contained" transcripts in the .combined.gtf file. come through, contained girlies ✨
• -F — do not discard intron-redundant transfrags if they share the 5' end (i.e. if they differ only at the 3' end). 🔥
• -G — generic GFF input file(s): do not assume Cufflinks GTF, and do not discard any intron-redundant transfrags. she's flexible like that 🦋
• -T — do not generate .tmap and .refmap files for each input file. less output, less clutter, self-care. 🧚
• -V — verbose processing mode (showing all GFF parsing warnings). she will tell you everything, and honestly? good for her. 😭

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💖 that's the whole vibe check, bestie. go cluster some transfrags, you're gonna ate. periodt.

sign-off: this was cuffcompare 2.2.1+dfsg.1-9, dated November 2021. mwah, take care of her 💅✨