genRandomReads - toolkit for processing next-gen sequencing data

        This manpage was written by Alexandre Mestiashvili for the Debian distribution and
        can be used for any other usage of the program.

genRandomReads 2.0.3                               March 2023                                  GENRANDOMREADS(1)

       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.

       genRandomReads - toolkit for processing next-gen sequencing data