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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.
Options
Output Ports
- Output filename for read-output, which contains the mapped annotations followed by their parent annotation. [gff]
- 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. [gff]
- Output filename for tuple-output, which contains exon tuples connected by reads or matepairs. [gff]
Views
- Insegt Std Output
- The text sent to standard out during the execution of Insegt.
- Insegt Error Output
- The text sent to standard error during the execution of Insegt. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)
Workflows
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Links
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Developers
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