table of contents
HOMGENEMAPPING(1) | HOMGENEMAPPING(1) |
NAME¶
homGeneMapping - create summary of gene homology
SYNOPSIS¶
homGeneMapping [options] --gtfs=gffilenames.tbl --halfile=aln.hal
DESCRIPTION¶
homGeneMapping takes a set of gene predictions of different genomes and a hal alignment of the genomes and prints a summary for each gene, e.g.
OPTIONS¶
Mandatory parameters¶
--halfile=aln.hal
--gtfs=gtffilenames.tbl
name_of_genome_1 path/to/genefile/of/genome_1 path/to/hintsfile/of/genome_1 name_of_genome_2 path/to/genefile/of/genome_2 path/to/hintsfile/of/genome_2 ... name_of_genome_N path/to/genefile/of/genome_N path/to/hintsfile/of/genome_N
Additional options¶
--cpus=N
--noDupes
--details
--halLiftover_exec_dir=DIR
--unmapped
--tmpdir=DIR
--outdir=DIR
--printHomologs=FILE
# 0 dana # 1 dere # 2 dgri # 3 dmel # 4 dmoj # 5 dper (0, jg4139.t1) (0, jg4140.t1) (1, jg7797.t1) (2, jg3247.t1) (4, jg6720.t1) (5, jg313.t1) (1, jg14269.t1) (3, jg89.t1) (5, jg290.t1) ... Two transcripts are in the same set, if all their exons/introns are homologs and their are no additional exons/introns. This option requires the Boost C++ Library
--dbaccess=db
EXAMPLE¶
homGeneMapping --noDupes --halLiftover_exec_dir=~/tools/progressiveCactus/submodules/hal/bin --gtfs=gtffilenames.tbl --halfile=msca.hal homGeneMapping --gtfs=gtffilenames.tbl --halfile=aln.hal --outdir=outdir --cpus=4
AUTHORS¶
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
ADDITIONAL DOCUMENTATION¶
An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.