.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH GENRANDOMREADS "1" "February 2020" "genRandomReads 2.0.0+dfsg-1~bpo10+1" "User Commands"
.SH NAME
genRandomReads \- helper tool from subread suite
.SH USAGE
.PP
For scanning a FASTA/gz file:
.IP
genRandomReads \fB\-\-transcriptFasta\fR <file>\e
.HP
\fB\-\-outputPrefix\fR <string> \fB\-\-expressionLevels\fR <file> [other options]
.TP
\fB\-\-summarizeFasta\fR
Only output the transcript names and lengths.
.TP
\fB\-\-transcriptFasta\fR <file>
The transcript database in FASTA/gz format.
.TP
\fB\-\-outputPrefix\fR <string>
The prefix of the output files.
.TP
\fB\-\-totalReads\fR
<int>        Total read/pairs in output.
.TP
\fB\-\-expressionLevels\fR <file>
Two column table delimited by <TAB>, giving the
wanted TPM values. Columns: TranscriptID and TPM
.TP
\fB\-\-readLen\fR <int>
The length of the output reads. 100 by default.
.TP
\fB\-\-totalReads\fR <int>
Total read/pairs in the output.
.TP
\fB\-\-randSeed\fR <int64>
Seed to generate random numbers. UNIXTIME is used
as the random seed by default.
.TP
\fB\-\-qualityRefFile\fR <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.
.TP
\fB\-\-floorStrategy\fR
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.
.TP
\fB\-\-pairedEnd\fR
Generate paired\-end reads.
.HP
\fB\-\-insertionLenMean\fR <float>,\-\-insertionLenSigma <float>,\-\-insertionLenMin <int>,
.TP
\fB\-\-insertionLenMax\fR <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
.TP
\fB\-\-simpleTranscriptId\fR
Truncate transcript names to the first '|' or space.
.TP
\fB\-\-truthInReadNames\fR
Encode the true locations of reads in read names.
.TP
\fB\-\-noActualReads\fR
Do not actually generate reads in fastq.gz files.