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.

       -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

       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.

       VERSION

              insegt version: 1.0 Last update 2012-09-11