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.