NAME

       genRandomReads - helper tool from subread suite

USAGE

       For scanning a FASTA/gz file:

              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.