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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.