Simulate RNA-seq reads

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Documentation for package ‘polyester’ version 1.26.0

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polyester-package Polyester: simulating RNA-seq reads including differential expression
add_error add sequencing error to simulated reads
add_gc_bias add GC bias to a count matrix
add_platform_error Simulate sequencing error using empirical error model
cdnaf Model of positional bias that can arise when RNA-seq is performed using protocols relying on cDNA fragmentation.
count_transcripts determine how many transcripts are annotated in a FASTA or GTF file
create_read_numbers Generate a simulated data set based on known model parameters
empirical_density Estimated distribution of fragment lengths
fpkm_to_counts Turn FPKMs from a ballgown object into estimated counts for transcripts
generate_fragments generate a set of fragments from a set of transcripts
getAttributeField extract a specific field of the "attributes" column of a data frame created from a GTF/GFF file
get_params Estimate zero-inflated negative binomial parameters from a real dataset
get_reads get sequencing reads from fragments
gtf_dataframe data frame (in gtf-inspired format) for chromosome 22, hg19
loessfit1 Empirical GC bias model, NA06985
loessfit2 Empirical GC bias model, NA12144
loessfit3 Empirical GC bias model, NA12776
loessfit4 Empirical GC bias model, NA18858
loessfit5 Empirical GC bias model, NA20542
loessfit6 Empirical GC bias model, NA20772
loessfit7 Empirical GC bias model, NA20815
model1 Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, read mate 1 of a pair
model2 Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, read mate 2 of a pair
model3 Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, single-end read
model4 Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, read mate 1 of a pair
model5 Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, read mate 2 of a pair
model6 Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, single-end read
model7 Empirical error model Roche/454 FLX Titanium, single-end read
NB Draw nonzero negative binomial random numbers
polyester Polyester: simulating RNA-seq reads including differential expression
reverse_complement reverse-complement some fragments
rnaf Model of positional bias that can arise when RNA-seq is performed using protocols relying on RNA fragmentation.
seq_gtf Get transcript sequences from GTF file and sequence info
simulate_experiment simulate RNA-seq experiment using negative binomial model
simulate_experiment_countmat Simulate RNA-seq experiment
simulate_experiment_empirical Simulate RNA-seq experiment based on abundances from a data set
write_reads write sequencing reads to disk