table of contents
HOMGENEMAPPING(1) | HOMGENEMAPPING(1) |
NAME¶
homGeneMapping - create summary of gene homologySYNOPSIS¶
homGeneMapping [options] --gtfs=gffilenames.tbl --halfile=aln.halDESCRIPTION¶
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.•how many of its exons/introns are in agreement
with genes of other genomes
•how many of its exons/introns are supported by
extrinsic evidence from any of the genomes
•a list of geneids of homologous genes
OPTIONS¶
Mandatory parameters¶
--halfile=aln.halinput hal file
--gtfs=gtffilenames.tbl
a text file containing the locations of the input gene
files and optionally the hints files (both in GTF format). The file is
formatted as follows:
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=NN is the number of CPUs to use (default: 1)
--noDupes
do not map between duplications in hal graph. (default:
off)
--halLiftover_exec_dir=DIR
Directory that contains the executable halLiftover If not
specified it must be in $PATH environment variable.
--tmpdir=DIR
a temporary file directory that stores lifted over files.
(default 'tmp/' in current directory)
--outdir=DIR
file direcory that stores output gene files. (default:
current directory)
--printHomologs=FILE
prints disjunct sets of homologous transcripts to FILE,
e.g.
# 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