bam2hints - convert mRNA-to-genome alignments in BAM format into a hint file for
[parameters] --in=example.bam --out=hints.gff
The input BAM file must be sorted by target (=genome) sequence names and within
the sequences by begin coordinates.
priority of hint group (set to 4)
gaps at most this length are simply closed
(set to 14)
alignments with gaps shorter than this and
longer than maxgaplen are discarded (set to 32)
alignments with longer gaps are discarded (set
minimum length of a 'dangling' exon (set to
maximum length of gap in query (cDNA) sequence
(set to 5)
compute exonpart, exon and splice site hints
in addition to intron hints (set to 0=Off). You should generate exonpart hints
from RNA-Seq using wiggle (.wig) input to wig2hints.
this many bp are cut off of each exonpart hint
at end of alignment (set to 10)
source identifier (set to 'E')
only retrieve intron hints (e.g. because the
exon(part) hints are retrieved by converting to a wig track, set to 1=On).
Deprecated as this is the default now.
do not summarize multiple identical intron
hints to a single one (set to 0=Off)
only keep the strongest hint for a region (set
maximal number of hints at a given position
(0: filtering deactivated). A high value causes long running time of AUGUSTUS
in regions with thousands of cDNA alignments. (set to 0)
include splice site (dss, ass) hints in output
(set to 0=Off)
include splice sites hints from the ends of a
truncated alignment (contig too short, set to 0=Off)
fill this number in in the score column (set
alignments of the same clone are considered to
be of the same gene if not separeted by more than this (set to 400000).
Alignments that span more than this are ignored, but better filter long
introns through an alignment program.
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and
An exhaustive documentation can be found in the file