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gffread - component of cufflinks suite

GFFREAD(1) User Commands GFFREAD(1)

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
November 2017 gffread 2.2.1+dfsg.1-2