Provided by: cufflinks_1.3.0-1ubuntu2_amd64 bug

NAME

       gffread - one of the cufflinks tools

SYSNOPSIS

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

              [-o    <outfile.gff>]    [-t    <tname>]    [-r   [[<strand>]<chr>:]<start>..<end>]
              [-CTVNMAFGRUVBHSZWTOE] [-w <spl_exons.fa>] [-x <spl_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 mRNA/EST/protein
              mappings with -A option)

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

       -r     only   show   transcripts   crossing   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 given
              range

       -U     discard single-exon transcripts

       -C     discard mRNAs that have no CDS feature

       -F     keep all attributes from last column of GFF/GTF

       -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 non-transcript GFF records as well (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     only show multi-exon mRNAs if all  their  introns  have  the  typical  splice  site
              consensus ( GT-AG, GC-AG or AT-AC )

       -M     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)

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

       -S     sort  output  GFF  records by genomic sequence and start coordinate (this option is
              automatically enabled by -g option)

       -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

       -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

       Invalid argument: --help

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

              [-o   <outfile.gff>]    [-t    <tname>]    [-r    [[<strand>]<chr>:]<start>..<end>]
              [-CTVNMAFGRUVBHSZWTOE]  [-w  <spl_exons.fa>] [-x <spl_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  mRNA/EST/protein
              mappings with -A option)

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

       -r     only    show    transcripts    crossing   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  given
              range

       -U     discard single-exon transcripts

       -C     discard mRNAs that have no CDS feature

       -F     keep all attributes from last column of GFF/GTF

       -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  non-transcript GFF records as well (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     only  show  multi-exon  mRNAs  if  all  their  introns have the typical splice site
              consensus ( GT-AG, GC-AG or AT-AC )

       -M     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)

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

       -S     sort output GFF records by genomic sequence and start coordinate  (this  option  is
              automatically enabled by -g option)

       -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

       -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