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 Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.