simulate_experiment_countmat

path to FASTA file containing transcripts from which to simulate
reads. See details.

fasta

path to GTF file containing transcript structures from which reads
should be simulated. See details.

path to folder containing one FASTA file (<code>.fa</code>
extension) for each chromosome in <code>gtf</code>. See details.

seqpath

matrix with rows representing transcripts and columns
representing samples. Entry i,j specifies how many reads to simulate from
transcript i for sample j.

readmat

character, path to folder where simulated reads should be
written, without a slash at the end of the folder name. By default, reads
written to the working directory.

outdir

Mean RNA fragment length. Sequences will be read off the
end(s) of these fragments.

fraglen

fragsd

readlen

Sequencing error rate. Must be between 0 and 1. A uniform
error model is assumed.

error_rate

If <code>TRUE</code>, paired-end reads are simulated; else single-end
reads are simulated.

paired

Optional seed to set before simulating reads, for
reproducibility.

seed

Further arguments to pass to <code>seq_gtf</code>, if <code>gtf</code> is not
<code>NULL</code>.


create FASTA files containing RNA-seq reads simulated from provided
  transcripts, with optional differential expression between two groups
  (designated via read count matrix)


This package can be used to simulate RNA-seq reads from
differential expression experiments with replicates. The reads
can then be aligned and used to perform comparisons of methods
for differential expression.

Alyssa Frazee

polyester

Simulate RNA-seq reads

simulate_experiment_countmat function

create FASTA files containing RNA-seq reads simulated from provided
  transcripts, with optional differential expression between two groups
  (designated via read count matrix)

simulate_experiment_countmat: Simulate RNA-seq experiment

Description

Usage

Arguments

Value

Details

Examples