NAME

       cuffcompare - component of cufflinks suite

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)