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gt-tagerator - Online in the Cloud

Run gt-tagerator in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gt-tagerator that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 <[email protected]>.

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