GENRANDOMREADS(1) | User Commands | GENRANDOMREADS(1) |
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.
May 2020 | genRandomReads 2.0.1+dfsg |