Provided by: subread_1.6.5+dfsg-1_amd64 bug


       genRandomReads - helper tool from subread suite


       For scanning a FASTA/gz file:

              genRandomReads --transcriptFasta <file>\

       --outputPrefix <string> --expressionLevels <file> [other options]

              Only output the transcript names and lengths.

       --transcriptFasta <file>
              The transcript database in FASTA/gz format.

       --outputPrefix <string>
              The prefix of the output files.

              <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.

              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.

              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

              Truncate transcript names to the first '|' or space.

              Encode the true locations of reads in read names.

              Do not actually generate reads in fastq.gz files.