mRNA and DNA reads

Simulate both DNA and RNA-seq data with specified transcript abundances in order to benchmark allele-specific expression algorithms.

Inputs:

1. Reference file (fasta)
2. GFF (Gene and transcript coordinates)
3. dbSNP database.

Outputs:

1. Paired-end DNA fastq files
2. Paired-end mRNA fastq files
3. TSV file with SNPs

Description

From the GFF file we take exon coordinates and intersect them with the dbSNP to select SNPs that belong to exons. We also add a number of random SNVs per exon and we randomly assign a phase to each mutation. Then, we create two contigs (haplotypes) from a reference contig by introducing mutations based on the phase value.