Man page - insegt(1)
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- rabema_build_gold_standard(1)
- razers3(1)
- alf(1)
- stellar(1)
- rabema_evaluate(1)
- insegt(1)
- tree_recon(1)
- sak(1)
- rabema_prepare_sam(1)
- mason_materializer(1)
- yara_mapper(1)
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- micro_razers(1)
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- mason_genome(1)
- seqan_tcoffee(1)
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- razers(1)
Package: seqan-apps
apt-get install seqan-apps
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Manual
| INSEGT(1) | INSEGT(1) |
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.
| insegt 1.1.10 [tarball] |