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