Command
$ flux -t simulator -xlsp myParameters.par
myParameters.par
| REF_FILE_NAME | /Users/micha/annotations/hg19_RefSeq_2009-05-13.gtf | |
POLYA_SHAPE | 5 | |
POLYA_SCALE | 100 | |
| FRAG_METHOD | NB | |
| FRAG_SUBSTRATE | DNA | |
| FILTERING | ON | |
| READ_LENGTH | 75 | |
| PAIRED_END | TRUE | |
Explanation
The example carries out a complete simulation pipeline (flags "-xls") on the RefSeq annotation. RNA molecules are simulated with about normally distributed polyA-tail lengths of an average size of 100nt. Fragmentation by nebulization (FRAG_METHOD NB) is carried out after reverse transcription (FRAG_SUBSTRATE DNA). The default size selection is carried out (FILTERING ON). Finally, 75nt paired-end reads are obtained from the fragments.
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