NAME
gmap - Genomic Mapping and Alignment Program
SYNOPSIS
gmap -dDB|-gFASTA [OPTION]... [QUERY]...
DESCRIPTION
Align the sequences QUERY to the reference, specified with -d or -g.
With no QUERY, read standard input.
OPTIONS
Input options
-D, --dir=directory
Genome directory
-d, --db=STRING
Genome database. If argument is ’?’ (with the quotes), this
command lists available databases.
-G, --genomefull
Use full genome (all ASCII chars allowed; built explicitly
during setup), not compressed version
-g, --gseg=filename
User-suppled genomic segment
-q, --jobdiv=INT/INT
Process only i out of every n sequences e.g., 0/100 or 99/100
Computation options
-B, --batch=INT
Batch mode (0 = no pre-loading, 1 = pre-load only indices; 2
(default) = pre-load both indices and genome)
-K, --intronlength=INT
Max length for one intron (default 1000000)
-L, --totallength=INT
Max total intron length (default 2400000)
-x, --chimera_margin=INT
Amount of unaligned sequence that triggers search for a chimera
(default off)
-w, --reference=filename
Reference cDNA sequence for relative alignment
-t, --nthreads=INT
Number of worker threads
-s, --altstrain
Search alternate strains in addition
-C, --chrsubsetfile=filename
User-suppled chromosome subset file
-c, --chrsubset=string
Chromosome subset to search
-z, --direction=STRING
cDNA direction (sense, antisense, or auto (default))
-H, --trimendexons=INT
Trim end exons with fewer than given number of matches (in nt,
default 12)
-X, --canonical=INT
Reward for canonical and semi-canonical introns 0=low reward,
1=high reward (default), 2=low reward for high-identity
sequences and high reward otherwise
-p, --prunelevel
Pruning level: 0=no pruning (default), 1=poor seqs, 2=repetitive
seqs, 3=poor and repetitive
Output types
-S, --summary
Show summary of alignments only
-A, --align
Show alignments
-3, --continuous
Show alignment in three continuous lines
-4, --alignedexons
Show alignment in three lines per exon
-Z, --compress
Print output in compressed format
-E, --exons=STRING
Print exons ("cdna" or "genomic")
-P, --protein_dna
Print protein sequence (cDNA)
-Q, --protein_gen
Print protein sequence (genomic)
-f, --format=INT
Format for output
1 = PSL (BLAT) format,
2 = GFF3 gene format,
3 = GFF3 match format,
6 = splicesites output (for GSNAP),
7 = IIT FASTA exon map format,
8 = IIT FASTA map format,
9 = coords in table format
Output options
-n, --npaths=INT
Maximum number of paths to show. If set to 0, prints two paths
if chimera detected, else one.
-O, --ordered
Print output in same order as input (relevant only if there is
more than one worker thread)
-5, --md5
Print MD5 checksum for each query sequence
-o, --chimera_overlap
Overlap to show, if any, at chimera breakpoint
-V, --usesnps=STRING
Use database containing known SNPs (in <STRING>.iit, built
previously using snpindex) for reporting output
-F, --fulllength
Assume full-length protein, starting with Met
-T, --truncate
Truncate alignment around full-length protein, Met to Stop
Implies -F flag.
-Y, --tolerant
Translates cDNA with corrections for frameshifts
External map file options
-M, --mapdir=directory
Map directory
-m, --map=iitfile
Map file. If argument is ’?’ (with the quotes), this lists
available map files.
-e, --mapexons
Map each exon separately
-b, --mapboth
Report hits from both strands of genome
-u, --flanking=INT
Show flanking hits (default 0)
Alignment output options
-N, --nolengths
No intron lengths in alignment
-I, --invertmode=INT
Mode for alignments to genomic (-) strand:
0=Don’t invert the cDNA (default)
1=Invert cDNA and print genomic (-) strand
2=Invert cDNA and print genomic (+) strand
-i, --introngap=INT
Nucleotides to show on each end of intron (default=3)
-l, --wraplength=INT
Wrap length for alignment (default=50)
Help options
-v, --version
Show version
-?, --help
Show this help message
ENVIRONMENT
GMAPDB genome directory (eqivalent to -D)
FILES
~/.gmaprc
configuration file
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_setup(1), gsnap(1)
http://research-pub.gene.com/gmap/