.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH GENRANDOMREADS "1" "March 2023" "genRandomReads 2.0.3" "User Commands"
.SH NAME
genRandomReads \- toolkit for processing next-gen sequencing data
.SH 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.
.PP
Usage:
.IP
For scanning a FASTA/gz file:
.IP
\fI\,/usr/lib/subread/genRandomReads\/\fP \fB\-\-summarizeFasta\fR \e
.HP
\fB\-\-transcriptFasta\fR <file> \fB\-\-outputPrefix\fR <string> [\-\-simpleTranscriptId]
.IP
For generating read/pairs:
.IP
\fI\,/usr/lib/subread/genRandomReads\/\fP \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.
.SH AUTHOR
 This manpage was written by Alexandre Mestiashvili for the Debian distribution and
 can be used for any other usage of the program.