getTxVariantCounts

object

variants


For transcript variants, obtain counts of compatible fragments
extending across the start and/or end of each variant.
Variant frequencies are estimated based on representive counts.


RNA-seq data are informative for the analysis of known and
novel transcript isoforms. While the short length of RNA-seq
reads limits the ability to predict and quantify full-length
transcripts, short read data are well suited for the analysis
of individual alternative transcripts events (e.g. inclusion
or skipping of a cassette exon). The SGSeq package enables the
prediction, quantification and visualization of alternative
transcript events from BAM files.

getTxVariantCounts: Representative counts and frequency estimates for transcript variants

Description

Usage

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Examples