SimFFPE-package: NGS Read Simulator for FFPE Tissue
In LanyingWei/SimFFPE: NGS Read Simulator for FFPE Tissue

Description Details Author(s) See Also Examples

The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.

This package was not yet installed at build time.
The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRs), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCR). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples. To simplify the simulation, the genome is divided into small windows, and SRCRs are found within the same window (adjacent ss-DNA combination) or between different windows (distant ss-DNA simulation). For adjacent ss-DNA combination events, the original genomic distance between and strands of two combined SRCRs are also simulated based on real data. The simulation can cover whole genome, or several chromosomes, or large regions, or whole exome, or targeted regions. It also supports enzymatic / random fragmentation and paired-end / single-end sequencing simulations. Fine-tuning can be achieved by adjusting the parameters, and multi-threading is surported. Please check the package vignette for the guidance of fine-tuning

Index: This package was not yet installed at build time.
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There are three available functions for NGS read simulation of FFPE samples:

1. calcPhredScoreProfile: Calculate positional Phred score profile from BAM file for read simulation.

2. readSimFFPE: Simulate artifact chimeric reads on whole genome, or several chromosomes, or large regions.

3. targetReadSimFFPE: Simulate artifact chimeric reads in exonic / targeted regions.

NA

Maintainer: NA

calcPhredScoreProfile, readSimFFPE, targetReadSimFFPE

PhredScoreProfilePath <- system.file("extdata", "PhredScoreProfile2.txt",
                                     package = "SimFFPE")
PhredScoreProfile <- as.matrix(read.table(PhredScoreProfilePath, skip = 1))
colnames(PhredScoreProfile)  <- 
    strsplit(readLines(PhredScoreProfilePath)[1], "\t")[[1]]

referencePath <- system.file("extdata", "example.fasta", package = "SimFFPE")
reference <- readDNAStringSet(referencePath)

## Simulate reads of the first three sequences of the reference genome

sourceSeq <- reference[1:3]
outFile1 <- paste0(tempdir(), "/sim1")
readSimFFPE(sourceSeq, referencePath, PhredScoreProfile, outFile1, 
            coverage = 80, enzymeCut = TRUE, threads = 2)

## Simulate reads for targeted regions

bamFilePath <- system.file("extdata", "example.bam", package = "SimFFPE")
regionPath <- system.file("extdata", "regionsBam.txt", package = "SimFFPE")
regions <- read.table(regionPath)
PhredScoreProfile <- calcPhredScoreProfile(bamFilePath, targetRegions = regions)

regionPath <- system.file("extdata", "regionsSim.txt", package = "SimFFPE")
targetRegions <- read.table(regionPath)

outFile <- paste0(tempdir(), "/sim2")
targetReadSimFFPE(referencePath, PhredScoreProfile, targetRegions, outFile,
                  coverage = 80, readLen = 100, meanInsertLen = 180, 
                  sdInsertLen = 50, enzymeCut = FALSE)