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Code Block |
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$ flux -t simulator -xlsp myParameters.par |
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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 |
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READ_LENGTH |
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75 |
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PAIRED_END |
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TRUE |
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Section |
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Requires: REF_FILE_NAME, LOAD_CODING, LOAD_NONCODING The necessary first step in order to simulate the experiment is the loading of a reference annotation. Input data has to be in GTF format at the path specified by REF_FILE_NAME. Each transcript has to have "exon" features, LOAD_CODING takes into account the ones that have additionally "CDS" features, LOAD_NONCODING those which don't. Initiating the reading of the reference annotation (button "Run" in the toolbar) first causes a check whether the GTF structure is well sorted for efficiency of the subsequent operations. In case, the FLUX SIMULATOR will sort your file in the temporary directory, and subsequently a sorted copy of the file (with the suffix "_sorted" before the extension) should appear in the folder containing the project. Make sure to use sorted files instead of the original files in future runs, because file sorting can contribute a substantial part of the running time. Upon termination of reading and parsing the annotation, you see several statistics including a histogram of spliced transcript lengths (upper panel) and a zoom-in onto the first 3 quartiles (lower panel). This step also initiates the pro file by writing the first 4 columns, i.e., splice locus ID, transcript ID, CDS/NC and spliced transcript lengthThe 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. |