Introduction

CAMPAREE is an RNA expression simulator that is primed using real data to give realistic output. It estimates the signals as closely as possible from the real data, which then becomes the ground truth in the simulated data. For input, CAMPAREE requires RNA-Seq fastq files and, from the same organism, a reference genome with transcript level annotation. For each sample, CAMPAREE generates a simulated set of RNA transcripts mimicking expression levels from the fastq files and accounting for isoform-level differences and allele-specific expression. It also generates simulated diploid genomes and their corresponding annotations with phased SNP and indel calls from the fastq reads. Additionally, CAMPAREE outputs all underlying distributions used to simulate the expressed transcripts. The output transcripts are full-length RNA transcripts or pre-mRNA transcripts with introns included. If generating diploid data, since CAMPAREE infers parental genomes, it is necessary that each sample be derived from a single individual (rather than pooled RNA from multiple individuals).

This simulated transcriptome can then be used, for example, as input to an RNA-Seq simulator, or to generate idealized coverage plots.

ABOUT

CAMPAREE is being developed by the ITMAT Bioinformatics Laboratory in The Institute for Translational Medicine and Therapeutics, University of Pennsylvania.