NAME

genRandomReads - toolkit for processing next-gen sequencing data

DESCRIPTION

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:

For scanning a FASTA/gz file:

/usr/lib/subread/genRandomReads --summarizeFasta \

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

For generating read/pairs:

/usr/lib/subread/genRandomReads --transcriptFasta <file>\

--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.

AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.