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. -h, --help displays this help message. --version display version information options: : -ro, --read-output file output filename for read-output, which contains the mapped annotations followed by their parent annotation. valid filetype is: gff. -ao, --anno-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 file output filename for tuple-output, which contains exon tuples connected by reads or matepairs. valid filetype is: gff. -fo, --fusion-output str 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 int ntuple default: 2. -o, --offset-interval int offset to short alignment-intervals for search. default: 5. -t, --threshold-gaps int threshold for allowed gaps in alignment (not introns). default: 5. -c, --threshold-count int 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