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other versions
- bookworm 1.6.2+ds-3
- bookworm-backports 1.6.5+ds-2~bpo12+1
- testing 1.6.5+ds-2.2
- unstable 1.6.5+ds-2.2
GT-TAGERATOR(1) | GenomeTools Manual | GT-TAGERATOR(1) |
NAME¶
gt-tagerator - Map short sequence tags in given index.
SYNOPSIS¶
gt tagerator [options] -q tagfile [-esa|-pck] indexname
DESCRIPTION¶
-q
Specify files containing the short sequence tags
-e [value]
Specify the allowed number of differences
(replacements/insertions/deletions)
-esa [string]
Specify index (enhanced suffix array) (default:
undefined)
-pck [string]
Specify index (packed index) (default: undefined)
-nod [yes|no]
Do not compute direct matches (default: no)
-nop [yes|no]
Do not compute palindromic matches (i.e. no reverse
complemented matches.) (default: no)
-best [yes|no]
Compute only best matches, i.e. only for smallest edit
distance with matches (default: no)
-maxocc [value]
specify max number of match-occurrences (default:
0)
-skpp [yes|no]
Skip prefix of pattern (only in pdiff mode) (default:
no)
-withwildcards [yes|no]
output matches containing wildcard characters (e.g. N);
only relevant for approximate matching (default: yes)
-output
use combination of the following keywords to specify
output tagnum show ordinal number of tag tagseq show tag sequence dblength
show length of match in database dbstartpos show start position of match in
database abspos show absolute value of dbstartpos dbsequence show sequence of
match strand show strand edist show edit distance tagstartpos show start
position of match in tag (only for -maxocc) taglength show length of match in
tag (only for -maxocc) tagsuffixseq show suffix tag involved in match (only
for -maxocc)
-v [yes|no]
be verbose (default: no)
-help
display help and exit
-version
display version information and exit
REPORTING BUGS¶
Report bugs to <kurtz@zbh.uni-hamburg.de>.
01/31/2024 | GenomeTools 1.6.5 |