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gmap
Langue: en
Version: 335013 (ubuntu - 24/10/10)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
gmap - Genomic Mapping and Alignment ProgramSYNOPSIS
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. WatanabeREPORTING 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/
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre