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

cuffcompare v1.0.2 (2335)                           May 2011                                      CUFFCOMPARE(1)