DESCRIPTION

cuffcompare v2.2.1 () ----------------------------- Usage: 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>]}

Cuffcompare provides classification, reference annotation mapping and various statistics for Cufflinks transfrags. Cuffcompare clusters and tracks transfrags across multiple samples, writing matching transcripts (intron chains) into <outprefix>.tracking, and a GTF file <outprefix>.combined.gtf containing a nonredundant set of transcripts across all input files (with a single representative transfrag chosen for each clique of matching transfrags across samples).

OPTIONS

-i provide a text file with a list of Cufflinks GTF files to process instead

of expecting them as command line arguments (useful when a large number of GTF files should be processed)

-r a set of known mRNAs to use as a reference for assessing

the accuracy of mRNAs or gene models given in <input.gtf>

-R for -r option, consider only the reference transcripts that

overlap any of the input transfrags (Sn correction)

-Q for -r option, consider only the input transcripts that

overlap any of the reference transcripts (Sp correction); (Warning: this will discard all "novel" loci!)

-M discard (ignore) single-exon transfrags and reference transcripts -N discard (ignore) single-exon reference transcripts

-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 (100)

-d max. distance (range) for grouping transcript start sites (100) -p the name prefix to use for consensus transcripts in the

<outprefix>.combined.gtf file (default: 'TCONS')

-C include the "contained" transcripts in the .combined.gtf file -F do not discard intron-redundant transfrags if they share the 5' end

(if they differ only at the 3' end))

-G generic GFF input file(s): do not assume Cufflinks GTF, do not

discard any intron-redundant transfrags)

-T do not generate .tmap and .refmap files for each input file -V verbose processing mode (showing all GFF parsing warnings)