Provided by: cufflinks_2.1.1-4_amd64 
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
gffread Usage: May 2011 GFFREAD(1)