gmap

Langue: en

Version: 335013 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)

Sommaire

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 2005 Genentech, Inc. All rights reserved.

SEE ALSO

gmap_setup(1), gsnap(1)
http://research-pub.gene.com/gmap/