INSEGT is a tool to analyse alignments of RNA-Seq reads (single-end or paired-end) by using gene annotations. It can measure exon, transcript and gene expression levels of given annotations. If read alignments span more than one exon, INSEGT can also compute possible exon combinations (tuple) and their expression levels. According to requirements it computes maximal tuple or tuple with a certain length. For paired-end reads INSEGT builds also tuple, whose exons are connected by matepairs. Briefly it searches the intervals of the read alignments in the intervals of the given annotations. It counts the mapped reads for each annotation and its parent annotation and stores the mapped annotations for each read.
- Linux / MacOsX / Windows
:: MORE INFORMATION