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I am using your FLUX Simulator to generate RNA-Seq data. Because= I am investigating differential exon usage, I hope to simulate, say among = the genes in a real dataset, there are 1,000 genes have differential exon u= sages between two conditions. I only consider the simplest case of exon ski= pping, and the following files are available:
1. an annotation GTF file
2. BAM file for each sample (fr= om TopHat)
3. BED file for each sample (fr= om TopHat)
I studied the FLUX Simulator pages and examples, but I am not sure how t= o =E2=80=9Cpick up=E2=80=9D 1,000 genes (from these files available) and so= mehow modify them to contain differential exon usages (e.g. exon skipping i= n condition 1 only). I think what I need eventually are one GTF file, BAM f= ile for each sample, and BED file for each sample. The output of FLUX Simul= ator includes .BED and .FASTQ which I believe are relevant to what I need.<= /p>
Thank you in advance for your suggestions! I appreciate if you could pro= vide a toy example for this situation (e.g. .par file). Thanks!