insegt - INtersecting SEcond Generation sequencing daTa with
annotation
insegt [OPTIONS] <ALIGMENTS-FILE>
<ANNOTATIONS-FILE>
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.
- -h, --help
- Display the help message.
- --version
- Display version information.
- -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.