-i discard transcripts having an intron larger than <maxintron>
-l discard transcripts shorter than <minlen> bases
-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 features
--nc non-coding only: discard mRNAs that have CDS features
--ignore-locus : discard locus features and attributes found in the input
-A use the description field from <seq_info.fsize> and add it as the value for a 'descr' attribute to
the GFF record
-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)
Sorting: (by default, chromosomes are kept in the order they were found)
--sort-alpha : chromosomes (reference sequences) are sorted alphabetically
--sort-by : sort the reference sequences by the order in which their
names are given in the <refseq.lst> file
Miscoptions:-F attempt to preserve all GFF attributes preservation
--keep-exon-attrs : for -F option, do not attempt to reduce redundant
exon/CDS attributes
-G do not keep exon attributes, move them to the transcript feature (for GFF3 output)
--keep-genes : in transcript-only mode (default), also preserve gene records
--keep-comments: for GFF3 input/output, try to preserve comments
-O process other non-transcript GFF records (by default non-transcript records are ignored)
-V discard any mRNAs with CDS having in-frame stop codons (requires -g)
-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 (requires -g)
-P add transcript level GFF attributes about the coding status of each transcript, including
partialness or in-frame stop codons (requires -g)
--add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
that have CDS features
--adj-stop stop codon adjustment: enables -P and performs automatic
adjustment of the CDS stop coordinate if premature or downstream
-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 (i.e. only print mRNAs with a complete CDS)
--no-pseudo: filter out records matching the 'pseudo' keyword
--in-bed: input should be parsed as BED format (automatic if the input
filename ends with .bed*)
--in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
features (see --tlf option below); automatic if the input filename ends with .tlf)
Clustering:-M/--merge : cluster the input transcripts into loci, discarding
"duplicated" transcripts (those with the same exact introns and fully contained or equal
boundaries)
-d <dupinfo> : for -M option, write duplication info to file <dupinfo>
--cluster-only: same as -M/--merge but without discarding any of the
"duplicate" transcripts, only create "locus" features
-K for -M option: also discard as redundant the shorter, fully contained
transcripts (intron chains matching a part of the container)
-Q for -M option, no longer require boundary containment when assessing redundancy (can be combined
with -K); only introns have to match for multi-exon transcripts, and >=80% overlap for single-exon
transcripts
-Y for -M option, enforce -Q but also discard overlapping single-exon transcripts, even on the
opposite strand (can be combined with -K)
Outputoptions:--force-exons: make sure that the lowest level GFF features are considered
"exon" features
--gene2exon: for single-line genes not parenting any transcripts, add an
exon feature spanning the entire gene (treat it as a transcript)
-D decode url encoded characters within attributes
-Z merge very close exons into a single exon (when intron size<4)
-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)
-w write a fasta file with spliced exons for each GFF transcript
-x write a fasta file with spliced CDS for each GFF transcript
-y write a protein fasta file with the translation of CDS for each record
-W for -w and -x options, write in the FASTA defline the exon coordinates projected onto the spliced
sequence; for -y option, write transcript attributes in the FASTA defline
-S for -y option, use '*' instead of '.' as stop codon translation
-L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
-m <chr_replace> is a name mapping table for converting reference sequence names, having this
2-column format: <original_ref_ID> <new_ref_ID> WARNING: all GFF records on reference sequences
whose original IDs are not found in the 1st column of this table will be discarded!
-t use <trackname> in the 2nd column of each GFF/GTF output line
-o print the GFF records to <outfile.gff> (those that passed any given filters). Use -o- to enable
printing of to stdout
-T for -o, output will be GTF instead of GFF3
--bed for -o, output BED format instead of GFF3
--tlf for -o, output "transcript line format" which is like GFF
but exons, CDS features and related data are stored as GFF attributes in the transcript feature
line, like this:
exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
<exons> is a comma-delimited list of exon_start-exon_end coordinates; <CDScoords> is
CDS_start:CDS_end coordinates or a list like <exons>;
-v,-E expose (warn about) duplicate transcript IDs and other potential
problems with the given GFF/GTF records
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