NAME
gmap_setup - create a genome database for GMAP or GSNAP
SYNOPSIS
gmap_setup -dgenomename [-Ddestdir] [-oMakefile] FASTA
OPTIONS
-d genome name
-D destination directory for installation (defaults to gmapdb
directory specified at configure time)
-o name of output Makefile (default is "Makefile.<genome>")
-M use coordinates from an .md file (e.g., seq_contig.md file from
NCBI)
-C try to parse chromosomal coordinates from each FASTA header
-E interpret argument as a command, instead of a list of FASTA
files
-O order chromosomes in numeric/alphabetic order (0 = no, 1 = yes
(default))
Advanced options
-W write some output directly to file, instead of using RAM (use
only if RAM is limited)
-q GMAP indexing interval (default: 3 nt)
-Q PMAP indexing interval (default: 6 aa)
DESCRIPTION
If you want to treat each FASTA entry as a separate chromosome (either
because it is in fact an entire chromosome or because you have contigs
without any chromosomal information), you can simply call gmap_setup
like this:
gmap_setup -d <genome> <fasta_file>...
The accession of each FASTA header (the word following each ">") will
be the name of each chromosome. GMAP can handle an unlimited number of
"chromosomes", with arbitrarily long names. In this way, GMAP could be
used as a general search program for near-identity matches against a
FASTA file.
-M and -C
If your sequences represent contigs that have mapping
information to specific chromosomal regions, then you can have
gmap_setup try to read each header to determine its chromosomal
region (the -C flag) or read an .md file that contains
information about chromosomal regions (the -M flag). The .md
files are often provided in NCBI releases, but since the formats
change often, gmap_setup will prompt you to make sure it parses
it correctly.
-E If you need to pre-process the FASTA files before using these
programs, perhaps because they are compressed or because you
need to insert chromosomal information in the header lines, you
can specify a command instead of multiple fasta_files, like
these examples:
gmap_setup -d <genome> -E ’gunzip -c genomefiles.gz’
gmap_setup -d <genome> -E ’cat *.fa |
./add-chromosomal-info.pl’
-W The gmap_setup process works best if you have a computer with
enough RAM to hold the entire genome (e.g., 3 gigabytes for a
human- or mouse-sized genome). Since the resulting genome files
work across all machine architectures, you can find any machine
with sufficient RAM to build the genome files and then transfer
the files to another machine. (GMAP itself runs fine on
machines with limited RAM.) If you cannot find any machine with
sufficient RAM for gmap_setup, you can run the program with the
-W flag to write the files directly, but this can be very slow.
-q and -Q
If you specify a smaller interval (for example, 3 for the GMAP
interval), you can create a higher-resolution database, which
can be useful for mapping small oligomers (smaller than 18 nt).
However, the corresponding genome index files will be larger
(twice as big if you specify -q 3). These index files may
exceed the 2 gigabyte file offset limit on some computers, and
will therefore fail to work on those computers.
AUTHOR
Thomas D. Wu and Colin K. Watanabe
REPORTING BUGS
Report bugs to Thomas Wu <twu@gene.com>.
COPYRIGHT
Copyright 2005 Genentech, Inc. All rights reserved.
SEE ALSO
gmap(1), gsnap(1)
http://research-pub.gene.com/gmap/