genRandomReads1

Overview

Error: a transcript file must be provide. Error: the output prefix must be provide. Error: the wanted expression levels must be provided. Warning: no read number is specified. Generating one million reads.

Usage:

--transcriptFasta <file> --outputPrefix <string> [--simpleTranscriptId]

--outputPrefix <string> --expressionLevels <file> [other options]

--summarizeFasta

Only output the transcript names and lengths.

--transcriptFasta <file>

The transcript database in FASTA/gz format.

--outputPrefix <string>

The prefix of the output files.

--totalReads

<int> Total read/pairs in output.

--expressionLevels <file>

Two column table delimited by <TAB>, giving the wanted TPM values. Columns: TranscriptID and TPM

--readLen <int>

The length of the output reads. 100 by default.

--totalReads <int>

Total read/pairs in the output.

--randSeed <int64>

Seed to generate random numbers. UNIXTIME is used as the random seed by default.

--qualityRefFile <file>

A textual file containing Phred+33 quanlity strings for simulating sequencing errors. The quality strings have to have the same length as the output reads. No sequencing errors are simulated when this option is omitted.

--floorStrategy

How to deal with round-up errors. 'FLOOR': generate less than wanted reads; 'RANDOM': randomly assign margin reads to transcripts; 'ITERATIVE': find the best M value to have ~N reads.

--pairedEnd

Generate paired-end reads.

--insertionLenMean <float>,--insertionLenSigma <float>,--insertionLenMin <int>,

--insertionLenMax <int>

Parameters of a truncated normal distribution for deciding insertion lengths of paired-end reads. Default values: mean=160, sigma=30, min=110, max=400

--simpleTranscriptId

Truncate transcript names to the first '|' or space.

--truthInReadNames

Encode the true locations of reads in read names.

--noActualReads

Do not actually generate reads in fastq.gz files.