Man page - insegt(1)
Packages contains this manual
- rabema_evaluate(1)
- alf(1)
- mason_materializer(1)
- pair_align(1)
- gustaf(1)
- stellar(1)
- razers3(1)
- sak(1)
- yara_indexer(1)
- mason_frag_sequencing(1)
- micro_razers(1)
- rabema_prepare_sam(1)
- insegt(1)
- rabema_build_gold_standard(1)
- splazers(1)
- seqan_tcoffee(1)
- yara_mapper(1)
- tree_recon(1)
- mason_genome(1)
- mason_methylation(1)
- razers(1)
- snp_store(1)
apt-get install seqan-apps
Manual
INSEGT
NAMESYNOPSIS
DESCRIPTION
REQUIRED ARGUMENTS
OPTIONS
Options: :
EXAMPLES
NAME
insegt - INtersecting SEcond Generation sequencing daTa with annotation
SYNOPSIS
insegt [ OPTIONS ] < ALIGMENTS-FILE > < ANNOTATIONS-FILE >
DESCRIPTION
INSEGT is a tool to analyze alignments of RNA-Seq reads (single-end or paired-end) by using gene-annotations.
Input to INSEGT is a SAM file containing the alignments and a file containing the annotations of the reference genome, either in GFF or GTF format.
REQUIRED ARGUMENTS
ARGUMENT 0 INPUT_FILE
Valid filetype is: .sam .
ARGUMENT 1 INPUT_FILE
Valid filetypes are: .gtf and .gff .
OPTIONS
-h , --help
Display the help message.
--version
Display version information.
Options: :
-ro , --read-output OUTPUT_FILE
Output filename for read-output, which contains the mapped annotations followed by their parent annotation. Valid filetype is: .gff .
-ao , --anno-output OUTPUT_FILE
Output filename for anno-output, which contains the annotations similar to the GFF input and additionally the counts of the mapped reads and the normalized expression levels in RPKM. Valid filetype is: .gff .
-to , --tuple-output OUTPUT_FILE
Output filename for tuple-output, which contains exon tuples connected by reads or matepairs. Valid filetype is: .gff .
-fo , --fusion-output STRING
Output filename for fusion-output, which contains exon tuple of gene fusions (Advanced option, currently no output port for KNIME). One of gff .
-n , --ntuple INTEGER
ntuple Default: 2 .
-o , --offset-interval INTEGER
Offset to short alignment-intervals for search. Default: 5 .
-t , --threshold-gaps INTEGER
Threshold for allowed gaps in alignment (not introns). Default: 5 .
-c , --threshold-count INTEGER
Threshold for min. count of tuple for output. Default: 1 .
-r , --threshold-rpkm DOUBLE
Threshold for min. RPKM of tuple for output. Default: 0.0 .
-m , --max-tuple
Create only maxTuple (which are spanned by the whole read).
-e , --exact-ntuple
Create only Tuple of exact length n. By default all tuple up to the given length are computed (if -m is set, -e will be ignored).
-u , --unknown-orientation
Orientation of reads is unknown.
EXAMPLES
insegt example/alignments.sam example/annotations.gff
Run INSEGT on example files with default parameters.
insegt -m example/alignments.sam example/annotations.gff
Run INSEGT on example files and only compute maxTuple.
insegt -c 2 example/alignments.sam example/annotations.gff
Run INSEGT on example files and only output tuple with a min. count of 2.