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