Misc options:¶

-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)

Output options:¶

--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