NAME

       cuffcompare - helps analyze the transfrags

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>]}

DESCRIPTION

       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, reduce the set of reference transcripts to

              only those found to overlap any of the input 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

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

SEE ALSO

       http://cufflinks.cbcb.umd.edu/manual.html#cuffcompare