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GTHGETSEQ(1)   GTHGETSEQ(1)

NAME

gthgetseq - get FASTA sequences from GenomeThreader files

SYNOPSIS

gthgetseq -getcdna | -getprotein | -getgenomic [option ...] [file ...]

DESCRIPTION

Get FASTA sequences from GenomeThreader files containing intermediate results. The sequences are shown on stdout.

OPTIONS

-getcdna

get cDNA/EST sequences default: no

-getcdnacomp

get complement of cDNA/EST sequences default: no

-getprotein

get protein sequences default: no

-getproteincomp

get complement of protein sequences default: no

-getgenomic

get genomic sequences default: no

-getgenomiccomp

get complement of genomic sequences default: no

-minalignmentscore

set the minimum alignment score for spliced alignments to be included into the set of spliced alignments default: 0.00

-maxalignmentscore

set the maximum alignment score for spliced alignments to be included into the set of spliced alignments default: 1.00

-mincoverage

set the minimum coverage for spliced alignments to be included into the set of spliced alignments default: 0.00

-maxcoverage

set the maximum coverage for spliced alignments to be included into the set of spliced alignments default: 9999.99

-gzip

gzip compressed input file(s) default: no

-bzip2

bzip2 compressed input file(s) default: no

-help

display help and exit

-version

display version information and exit