NAME

       gffread - component of cufflinks suite

DESCRIPTION

       Usage: gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>]

              [-o <outfile.gff>] [-t <tname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]] [-CTVNJMKQAFGUBHZWTOLE]
              [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>] [-i <maxintron>]

       Filters and/or converts GFF3/GTF2 records.  <input_gff> is a GFF file, use '-' if the GFF records will be
       given at stdin

OPTIONS

       -g     full  path to a multi-fasta file with the genomic sequences for all input mappings, OR a directory
              with single-fasta files (one per genomic sequence, with file names matching sequence names)

       -s     <seq_info.fsize> is a tab-delimited file providing this info for each  of  the  mapped  sequences:
              <seq-name> <seq-length> <seq-description> (useful for -A option with mRNA/EST/protein mappings)

       -i     discard transcripts having an intron larger than <maxintron>

       -r     only  show  transcripts  overlapping  coordinate range <start>..<end> (on chromosome/contig <chr>,
              strand <strand> if provided)

       -R     for -r option, discard all transcripts that are not fully contained within the given range

       -U     discard single-exon transcripts

       -C     coding only: discard mRNAs that have no CDS feature

       -F     full GFF attribute preservation (all attributes are shown)

       -G     only parse additional exon attributes from the first exon and move them to the mRNA level  (useful
              for GTF input)

       -A     use the description field from <seq_info.fsize> and add it as the value for a 'descr' attribute to
              the GFF record

       -O     process also non-transcript GFF records (by default non-transcript records are ignored)

       -V     discard any mRNAs with CDS having in-frame stop codons

       -H     for  -V  option,  check  and  adjust  the  starting  CDS  phase  if  the original phase leads to a
              translation with an in-frame stop codon

       -B     for -V option, single-exon transcripts are also checked on the opposite strand

       -N     discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus (i.e. not
              GT-AG, GC-AG or AT-AC)

       -J     discard any mRNAs that either lack initial START codon or the terminal  STOP  codon,  or  have  an
              in-frame stop codon (only print mRNAs with a fulll, valid CDS)

       --no-pseudo: filter out records matching the 'pseudo' keyword

       -M/--merge : cluster the input transcripts into loci, collapsing matching

              transcripts (those with the same exact introns and fully contained)

       -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>

       --cluster-only: same as --merge but without collapsing matching transcripts

       -K     for  -M  option:  also  collapse  shorter, fully contained transcripts with fewer introns than the
              container

       -Q     for -M option, remove the containment restriction: (multi-exon transcripts will  be  collapsed  if
              just their introns match, while single-exon transcripts can partially overlap (80%))

       --force-exons: make sure that the lowest level GFF features are printed as

              "exon" features

       -E     expose  (warn  about) duplicate transcript IDs and other potential problems with the given GFF/GTF
              records

       -D     decode url encoded characters within attributes

       -Z     merge close exons into a single exon (for intron size<4)

       -w     write a fasta file with spliced exons for each GFF transcript

       -x     write a fasta file with spliced CDS for each GFF transcript

       -W     for -w and -x options, also write for each fasta record the exon coordinates  projected  onto  the
              spliced sequence

       -y     write a protein fasta file with the translation of CDS for each record

       -L     Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)

       -m     <chr_replace>   is   a   reference   (genomic)   sequence  replacement  table  with  this  format:
              <original_ref_ID> <new_ref_ID> GFF records on reference sequences that are  not  found  among  the
              <original_ref_ID> entries in this file will be filtered out

       -o     the "filtered" GFF records will be written to <outfile.gff> (use -o- for printing to stdout)

       -t     use <trackname> in the second column of each GFF output line

       -T  -o option will output GTF format instead of GFF3

gffread 2.2.1+dfsg.1-2                            November 2017                                       GFFREAD(1)