dupRadar

dupRadar is an R package which is part of the Bioconductor project . It requires mapped, duplicate marked RNA-Seq reads as a bam file and a gene annotation file in GTF format and produces a table with per gene values such as read counts, percentage of duplicate reads, normalized read counts. The package provides functions for plotting and analyzing the duplication rates dependent on the expression levels.

Install it from R with:

R> source("https://bioconductor.org/biocLite.R")
R> biocLite("dupRadar")

Features

RNA-Seq quality control
NGS PCR duplicate detection
Needs duplicate marked bam file and a reference GTF

Project Samples

Density of per gene duplication rates (good sample)

Density of per gene duplication rates (problematic sample)

Scatterplot of per gene duplication rate vs. expression / log10(RPK) on a dataset with a low amount of PCR artefacts.

Boxplot of duplication rates of gene expression bins on a dataset with a low amount of PCR artefacts.

Scatterplot of per gene duplication rate vs. expression / log10(RPK) on a dataset with a high amount of PCR artefacts.

Boxplot of duplication rates of gene expression bins on a dataset with a high amount of PCR artefacts.

Project Activity

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