GFFREAD(1)

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