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