insegt1
Intersecting second generation sequencing data with annotation
Usage
insegt [OPTIONS]
<ALIGMENTS-FILE>
<ANNOTATIONS-FILE>
Overview
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
|
Run INSEGT on example files with default parameters. |
|---|---|
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Run INSEGT on example files and only compute maxTuple. |
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Run INSEGT on example files and only output tuple with a min. count of 2. |
Releases
6 releases since Debian 8 (Jessie); the text changed 2 times.
--anno-output since Debian 10 (Buster);
--exact-ntuple since Debian 10 (Buster);
--fusion-output since Debian 10 (Buster);
--help since Debian 10 (Buster);
--max-tuple since Debian 10 (Buster);
--ntuple since Debian 10 (Buster);
--offset-interval since Debian 10 (Buster);
--read-output since Debian 10 (Buster);
--threshold-count since Debian 10 (Buster);
--threshold-gaps since Debian 10 (Buster);
--threshold-rpkm since Debian 10 (Buster);
--tuple-output since Debian 10 (Buster);
--unknown-orientation since Debian 10 (Buster);
--version since Debian 10 (Buster);
-ao since Debian 10 (Buster);
-c since Debian 10 (Buster);
-e since Debian 10 (Buster);
-fo since Debian 10 (Buster);
-h since Debian 10 (Buster);
-m since Debian 10 (Buster);
-n since Debian 10 (Buster);
-o since Debian 10 (Buster);
-r since Debian 10 (Buster);
-ro since Debian 10 (Buster);
-t since Debian 10 (Buster);
-to since Debian 10 (Buster);
-u since Debian 10 (Buster).