---
name: "genRandomReads"
section: "1"
platform: "linux"
package: "subread"
version: "2.0.8+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/genRandomReads"
---

# genRandomReads(1)

toolkit for processing next-gen sequencing data

## 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 Alexandre Mestiashvili for the Debian distribution and\
  can be used for any other usage of the program.