NAME

       cuffcompare - component of cufflinks suite

DESCRIPTION

       cuffcompare    v2.2.1    (Debian    package)   -----------------------------   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)

cuffcompare 2.2.1+dfsg.1-10                        August 2024                                    CUFFCOMPARE(1)