trusty (1) gffread.1.gz

Provided by: cufflinks_2.1.1-4_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